• TABLE OF CONTENTS
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 Front Cover
 Title Page
 Table of Contents
 List of Figures
 List of Tables
 Main
 A preliminary assessment of the...














Title: Ortega/Cedar River Basin, Florida, restoration : Work plan to assess sediment-containment dynamics
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Title: Ortega/Cedar River Basin, Florida, restoration : Work plan to assess sediment-containment dynamics
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Table of Contents
    Front Cover
        Front Cover
    Title Page
        Page i
    Table of Contents
        Page ii
        Page iii
    List of Figures
        Page iv
        Page v
    List of Tables
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    Main
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    A preliminary assessment of the effect of episodic events on sediment yield in Zone 3
        Page A-1
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        Page A-4
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Full Text



UFL/COEL-99/019


ORTEGA/CEDAR RIVER BASIN, FLORIDA, RESTORATION:
WORK PLAN TO ASSESS SEDIMENT-CONTAMINANT
DYNAMICS

Final Report


by



Ashish J. Mehta
Robert Kirby
and
Earl J. Hayter


February, 2000



Submitted to:

St. Johns River Water Management District
Palatka, FL 32178








UFL/COEL-99/019


ORTEGA/CEDAR RIVER BASIN, FLORIDA, RESTORATION: WORK PLAN TO
ASSESS SEDIMENT-CONTAMINANT DYNAMICS





Final Report




By


Ashish J. Mehta
Robert Kirby
Earl J. Hayter


Submitted to:
St. Johns River Water Management District
Palatka, FL 32178


February, 2000










TABLE OF CONTENTS


LIST OFFIGURES ......................................... ..... ........... iv
LIST OF TABLES .......................................................... vi
SYNOPSIS ................................................................. 1
ACKNOWLEDGMENT ...................................................... 1
1. PROBLEM STATEMENT ............................................... 2
2. PHYSICAL SETTING ............... ................................. 2
3. WATER QUALITY ................................................... 4
3.1 Ortega River ........................ ........... ................. 4
3.2 St. Johns River ................................................ 5
4. APPROACH ............ ...................... ................ ... ... 6
4.1 Task 1: Review of Information .................................... 6
4.2 Task 2: Recommendation ........................................ 11
4.3 Task 3: Work Plans ............................................. 14
4.3.1 Zones 1/2 WorkPlan ...................... ............... .. 14
4.3.1.1 Water Level, Velocity and Stage-discharge .............. 14
4.3.1.2 Wave Data ....................................... 14
4.3.1.3 Water Quality Sampling ........................... 15
4.3.1.4 Sediment and Contaminant Load Rating Curves ......... 15
4.3.1.5 Contaminant Source Identification .................... 16
4.3.1.6 Assess Need for Basin Water Quality Modeling .......... 16
4.3.2 Zones 2/3 Work Plan ....................................... 18
4.3.2.1 Bottom Sediment Sampling ........................ 19
4.3.2.2 Sediment Physical Property Distribution .............. 19
4.3.2.3 Organic Sediment Geochemical Property Distribution .... 19
4.3.2.4 Sediment-bound Contaminant Distribution ............. 19
4.3.2.5 Assess Need for Additional Coring .................... 20
4.3.2.6 Assess Need of Shallow Acoustic Bottom Profiling ....... 20









4.3.2.7 Assess Need of Bioaccumuation Risk Analysis ........... 20

4.3.2.8 Contaminant Source Assessment ...................... 20

4.3.3 Zone 3 Work Plan ...................................... 21

4.3.3.1 Sediment Transport Parameter Tests .................. 21

4.3.3.2 Sediment Code Revision ........................... 21

4.3.3.3 Contaminated Sediment Budget and Fate ............... 23

4.3.3.4 Restoration Alternatives Evaluation ................... 23

4.4 Task 4: Report ................. ............................... 24

REFERENCES .................................................... ........ 26


APPENDIX

A PRELIMINARY ASSESSMENT OF THE EFFECT OF EPISODIC EVENTS


ON SEDIMENT YIELD IN ZONE 3 AREA OF

ACCUMULATION OF CONTAMINATED SEDIMENT ..

A.1 Introduction .................................

A.2 River Flow Dynamics .........................

A.3 Sediment Fluxes ...............................

A.3.1 Open Flow Boundary Condition Specification ..

A.3.2 Bottom Boundary Condition Specification .....

A.3.3 Sediment Flux and Yield Simulations .........

A.4 Concluding Comments .........................

A.4.1 Flow Field ..............................

A.4.2 Bottom Sediment .......................

A.4.3 Suspended Sediment .....................


SIGNIFICANT


................ A -1

................ A -1

................ A -2

................ A -9

............... A -13

............... A -15

............... A-20

............... A-24

............... A-24

............... A -25

............... A-26








LIST OF FIGURES


FIGURE PAGE
1 Part of St. Johns River Water Management District, Florida, and the Ortega/Cedar
River area inclusive of a portion of the lower St. Johns River (main-stem) .......... .3
2 Lower St. Johns River basin and sub-basins upstream of Trout River (after Camp,
Dresser & McKee, 1992) ................................................. 6
3 Schematization of zones of influence relative to Ortega/Cedar River sediment-
contaminant dynamics assessment ......................................... 7
4 Ortega/Cedar River basin, sub-basins and notional zones ........................ 9
5 Ortega and Cedar Rivers and contiguous segment of the St. Johns River (main-stem)
..................................................................... 10
6 Assessment process for potential restoration alternatives ........................ 23
A.1 Numerical fine mesh grid for the Ortega and Cedar Rivers, Zone 3 .............. A-3
A.2 Numerical coarse mesh grid for the main-stem (part of Zone 2) and Zone 3 ....... A-3
A-3 Simulated peak ebb flow velocity vectors at mean river runoff condition in Zone 3 A-5
A-4 Simulated peak flood flow velocity vectors at mean river runoff condition in Zone 3 A-5
A-5 Simulated peak ebb flow velocity vectors at maximum river runoff condition in Zone
3 ........................................... ....................... A -6
A-6 Simulated peak flood flow velocity vectors at maximum river runoff condition in
Zone 3 ....................................................... .. A-6
A-7 Simulated Lagrangian residual current velocity vectors at mean river runoff condition
in Zone 3 ..................................................... .. A-7
A-8 Sites for simulated peak velocities near the bottom reported in Table A.2 ......... A-7
A-9 Simulated peak ebb flow velocity vectors at mean runoff condition in the main-stem
and Zone 3 ....................................................... A-10
A-10 Simulated peak flood flow velocity vectors at mean runoff condition in the main-
stem and Zone 3 ................................................... A-10
A-11 Simulated peak ebb flow velocity vectors at maximum runoff in the main-stem and
Zone 3 ........................................................ A-11








A-12 Simulated peak flood flow velocity vectors at maximum runoff condition in the
main-stem and Zone 3 ............................................ A-11
A-13 Sites for output of simulated maximum velocities near the bottom in the main-stem
.................................................................. A -12
A-14 Sediment rating curves TSS as a function of bottom shear stress. Circles are based
on data ............................................................ A-14
A-15 Resuspension due to 0.55 m high and 3 s period waves at the mouth of the Ortega
River. The plot shows suspended sediment concentration profile evolution with time,
starting with zero initial concentration .................................. A-14
A-16 Sites of collection of bottom sediment grab samples ......................... A-16
A-17 Bottom erosion rate data: Sample 39B ................................... A-17
A-18 Bottom erosion rate data: Sample 10B ................................ A-17
A-19 Bottom erosion rate data: Sample 4B .................................. A-18
A-20 Bottom erosion rate data: Sample 4A .................................. A-18
A-21 Bottom erosion rate data: Sample 20A ................................. A-19
A-22 Cumulative bottom erosion rate data ................................... A-19
A-23 Sites of bottom sediment accumulation rate data ........................... A-20
A-24 Cross-sections at which sediment fluxes are simulated ....................... A-24
A-25 Tentative measurement locations for water level (tide gage), waves (pressure gage),
water quality and bottom coring ....................................... A-26
A-26 Cross-sections for current and turbidity measurements by ADCP .............. A-27








LIST OF TABLES


TABLE PAGE
1 Task numbers and titles ................................................. 24
2 Task numbers, durations and costs ........... ............................ 25
A.1 River runoff, tidal range and storm surge at the modeled domain boundaries ...... A-4
A.2 Peak ebb and flood near-bottom velocities at selected sites in Zone 3 ............ A-8
A.3 Peak ebb and flood near-bottom velocities at selected sites in the main-stem ..... A-12
A.4 Bottom sediment data: densities, organic content, erosion rate constant and settling
velocity ........................................................... A-15
A.5 Measured and simulated sedimentation rates ............................... A-21
A.6 Calculated sediment yield at selected cross-sections in Zone 3 ................. A-22
A.7 Calculated sediment yield at selected cross-sections in Zone 3 under mean runoff
along with waves and storm surge in the main-stem ......................... A-23
A-8 Sediment import-export relative to Zone 3 ................................ A-25








SYNOPSIS
This report presents a work plan developed under Phase 1 of a study to assess sediment-
contaminant dynamics in the Ortega/Cedar River basin. Implementation of the work plan is to be
carried out under Phase 2. In order to identify the sources and the fate of contaminated sediment,
especially with regard to the region of heavy accumulation of fine-grained material in the lower
reaches of the basin, the watershed is notionally subdivided into three overlapping zones. Based on
this subdivision, a three year primary study, extendable by an additional year, is recommended.
Extension is dependent on the need for secondary studies. This need must be assessed as part of the
primary study. The evaluation of the problem, as reported, is contingent upon three factors: 1) the
project statement, in particular related to "feasible and cost-effective approach and work for
conducting a study that will provide information needed to develop a sediment contaminant
restoration plan for Cedar and Ortega Rivers and watersheds", 2) initial and subsequent discussions
with SJRWMD staff regarding the zone of emphasis where restoration is a critical issue, namely the
lower Ortega River (including the lower Cedar River) and the contiguous waters of the St. Johns
River (i.e., main-stem), and 3) the directive by the St. Johns River Water Management District
(SJRWMD) staff to develop a plan independent of any potential participation by SJRWMD. Costs
included for all itemized tasks in Phase 2 are estimates. The total estimate for primary studies is
$399,250, with (very approximately) $256,150 for monitoring, $64,100 for modeling, $62,000 for
assessment and $17,000 for reporting. Finally, it needs to be noted that in the context of costs and
all other aspects, this report does not constitute a formal proposal for further work under Phase 2 by
the University of Florida.


ACKNOWLEDGMENT
We thank Dr. Del Bottcher and Dr. James Stuck of Soil & Water Engineering Technology,
Inc., Gainesville, Florida for their assistance in highlighting some of the important physical and
biogeophysical components of the river system. Thanks are due to Dr. Fred Morris, Mr. John
Higman and Dr. V. Chandy John of SJRWMD for extensive discussions and for supplying necessary
data. Dr. Getachew Belaineh coordinated our effort with SJRWMD. Dr. J. Jiang carried out the
numerical model application described in the Appendix. Ms. Alyson Baird and Ms. Brooke Hedlund
conducted the erosion tests. This study was supported by SJRWMD under contract no. 99B290.








ORTEGA/CEDAR RIVER BASIN, FLORIDA, RESTORATION: STUDY PLAN TO
ASSESS SEDIMENT-CONTAMINANT DYNAMICS


1. PROBLEM STATEMENT
The St. Johns River Water Management District (SJRWMD) has identified the Ortega/
Cedar Rivers in north Florida (Figure 1) to be heavily contaminated with polychlorinated byphenyls
(PCBs), polycyclic aromatic hydrocarbons (PAHs), heavy metals such as mercury and cadmium, and
pesticides. Cedar River, which is the smaller of the two, runs through an industrial zone within the
city of Jacksonville, and is believed to be a greater source of these contaminants than the Ortega
River. A significant source of the PCBs is believed to be an industrial lot in the proximity of Cedar
River (Environmental Protection Board, 1985). The PAHs are derived from various point and non-
point sources ultimately associated with petroleum hydrocarbons. Both PCBs and PAHs have high
particle affinity, and their rates of biogeochemical degradation are low (Towner, 1994). Heavy
metals show a similar affinity (Hayter and Pakala, 1989). The sources of these contaminants, their
transport to the St. Johns River, and the extent and degree of contamination, are not well known.
This information is needed to develop a watershed sediment-contaminant remediation plan for the
Ortega/Cedar River basin. The overall direction for this work is embedded in the State of Florida's
Surface Water Improvement and Management Act, Sections 373.451-373.4595 (Campbell et al.,
1993b).
The objective of this investigation is to develop a feasible and cost effective approach and
work plan for conducting a study that will provide information needed to develop a sediment-
contaminant restoration plan for the Ortega/Cedar River basin. The overall study is divided into two
phases, a planning phase (Phase 1) and an implementation phase (Phase 2). Under contract between
SJRWMD and the University of Florida, this report is concerned with Phase 1, with the primary aim
to develop an implementation plan to be carried out under Phase 2. In what follows, the physical
setting of the area, water quality, study approach and work plan for Phase 2 are described.


2. PHYSICAL SETTING
The Ortega River basin is located west of the St. Johns River in south-central Duval County
in northern Florida (Figure 1). The upstream portion of the Ortega River is known as McGirts Creek.








This creek lies within the Duval uplands physiographic province and flows generally north to south.
The Ortega River continues this course until it reaches the Eastern Valley physiographic province,
where the river gradually turns nearly 180 degrees to a north-northeasterly course before reaching
the St. Johns River north of the Jacksonville Naval Air Station. Elevations range from nearly 27 m
(NGVD) in the Duval uplands to nearly mean sea level near the St. Johns River.


Figure 1 Part of St. Johns River Water
Management District, Florida, and the
Ortega/Cedar River area inclusive of a portion
of the lower St. Johns River (main-stem).

Cedar River, the largest tributary of the Ortega River, is actually a major system itself. From
its headwaters north of Interstate 10 and west of Interstate 295, this river flows southeast to its








confluence with the Ortega River. Major tributaries to the Cedar are Willis Branch, Williamson
Creek, Butcher Pen Creek and Fishing Creek. The tidal interface for the Ortega River is at Collins
Road, while the tidal interface for Cedar River is near Lane Avenue. (These two and other road
locations are not highlighted in any drawings herein; they are found in road maps of the Jacksonville
area.)
In the early 1990s, approximately one-third of the Ortega/Cedar River basin was residential,
with commercial/industrial and vacant land comprising the other major land uses: Since then, vacant
land has decreased significantly. The following three soil mapping units are found within the basin:
Leon-Ortega, Leon-Ridgeland-Wesconnett, and Pelham-Mascotte-Sapelo. Depth to water table is
generally less than -1.5 m. However, in the proximity of the Interstate 295 corridor, this depth varies
between -1.5 to ~3 m (Camp, Dresser & McKee, 1989; 1992).


3. WATER QUALITY
3.1 Ortega River
According to Camp, Dresser & McKee (1992), seven tentative BESD (Bio-Environmental
Services Division of the Jacksonville Department of Health, Welfare and Bio-Environmental
Services) non-point source monitoring sites have been located within the Ortega River basin. Three
of these sites are along McGirts Creek/Ortega River, and four are in the Cedar River tributary
system. Two BESD water quality sampling stations are in the basin one on the Ortega River at
Timuquana Road and one on the Cedar River at Blanding Boulevard. The Florida Department of
Environmental Protection (FDEP) has one sampling station at the mouth of the Ortega River. The
U.S. Geological Survey (USGS) maintains a stage recorder on the Ortega River at the bridge for
103rd Street, upstream of the tidal interface. There are two crest-stage recorders in the basin one
on Williamson Creek and one on South Fork Wills Branch. Daily rainfall recorders at the
Jacksonville Naval Air Station (NAS) and the Cecil NAS are the nearest rain gage sites.
Presently, water quality data are being collected in Cedar River, Trout Creek and McCoy's
Creek on monthly, quarterly and annual basis as well as on an episodic basis. Daily or weekly
sampling is however not carried out (John Higman, SJRWMD, personal communication).
Several water quality nuisances have been identified, and a number of serious water quantity
problem effluent structures have been noted in the study area. Cedar River and much of Ortega River








have experienced a significant number of bacteriological water quality violations, thereby making
them water quality problem areas. Septic tank problem areas have been found within the Ortega
River basin. Such problems can be exacerbated by flooding, especially as the region becomes
increasingly urbanized. Under extreme events significant flooding has occurred. For example, in
1964 during Hurricane Dora, one of the most devastating hurricanes to affect northeastern Florida,
a storm surge of 1.8 m (NGVD) in the lower St. Johns River combined with runoff from Cedar River
basin raised water levels to well over 1.8 m at the mouth of Willis Branch. The largest single-day
rainfall from that event was 22.9 cm on September 10 at Jacksonville Heights at the southern
boundary of the Willis Branch drainage basin. Flooding was estimated to be about 1 in 10 years
frequency in the upper part of Willis Branch and 1 in 100 years, or greater, in the tidal reach near the
mouth (U. S. Army Corps of Engineers, 1995).


3.2 St. Johns River
According to Campbell et al. (1993a,b), the water quality of the lower St. Johns River in the
vicinity of the Ortega River mouth can be classified as poor. The FDEP has reported high levels of
turbidity, and bacterial and total phosphorus concentrations. Bank development has caused reduced
drainage. The Jacksonville NAS is located within this zone. Just north of the confluence of the
Ortega and Cedar Rivers, the St. Johns River turns 90 degrees east and then back north within a 4.5
km stretch (Figure 2). Both banks are almost entirely bulkheaded and lined with industries and urban
development.
The St. Johns River receives contaminants from a number of point and non-point sources.
Petrochemicals, heavy metals, phosphates and treated domestic wastewater are some of the
contaminants that occur in this area (Dixon, 1998). Heavy metal concentrations in sediments are
believed to be high, in part due to sandblasting of toxic paint from vessel hulls. Two noteworthy
point sources are believed to be the Buckman Street Waste Water Treatment Plant and the Jefferson
Smurfit, formerly Alton Box and Packaging, Corporation (Hand and Paulic, 1992). Ground water
contamination is also prevalent (Halford, 1999).



































Figure 2 Lower St. Johns River basin and sub-basins
upstream of Trout River (after Camp, Dresser & McKee,
1992).



4. APPROACH
The approach adopted in this (Phase 1) study follows the four tasks identified in the Scope
of Work within the agreement between SJRWMD and the University of Florida for the Cedar and
Ortega Rivers sediment-contaminant dynamics study plan.


4.1 Task 1: Review of Information
Literature review pertinent to the study is interspersed within the text of the report, and is
cited where necessary. A list of references is provided at the end of the report. A key conclusion we
have reached in this regard is that the available cumulative data base is presently insufficient to








enable even a preliminary assessment of site-specific restoration alternatives. This conclusion is

supported by the analysis carried out in the Appendix, in which we conclude that the data base is

inadequate to establish a budget for the contaminated sediment in the problem area. Such a budget,

especially with regard to the sources and sinks of contaminants and contaminated sediment, must

be established as a basis for the development of restoration options.

As part of the Phase 1 study, following preliminary discussions with SJRWMD staff, it was

concluded that to develop the work plan for Phase 2, a preliminary mathematical model study would

be a useful tool to understand the dynamics of contaminated sediment within and beyond the basin,

thus assisting in the development of a future study strategy including data needs for contaminated

sediment sourcing and fate. Accordingly, information provided by SJRWMD and from other sources

was reviewed and assimilated in two ways: 1) within the framework of modeling, and 2) within the

framework of the recommended work study plan. The first is described in the Appendix, while the

second is covered under Section 4.3.

With regard to contaminated sediment, two broadly based questions need to be addressed,

namely: 1) that related to source of sediment, and 2) that related to the fate of this sediment. In that

regard, Figure 3 shows a schematic drawing of the river basin.


Zone 3 (Significant
contaminated sediment
accumulation)








II
g.




Zone 2 (Tide-dominated source of
contaminants and sediment
contiguous to Zone 3)
Zone 1 (Watershed numerous point
and non-point sources of contaminants)

Figure 3 Schematization of zones of influence relative to
Ortega/Cedar River sediment-contaminant dynamics
assessment.











To ultimately address the above two questions, the entire domain of Figure 3 is notionally
sub-divided into three zones as follows:


Zone 1: Includes the entire watershed, which acts as the contaminant source for the
lower Ortega River. This zone is relatively well defined by the boundaries of the
watershed.
Zone 2: Includes the tide-dominated region surrounding the primary zone of
accumulation of contaminated sediment in the lower reaches of the Ortega and Cedar
Rivers. The boundary of this zone is not well defined, since it also includes waters
of the St. Johns River that are associated with the exchange of contaminated
sediment with the zone of accumulation of sediment in the lower Ortega River. For
a better definition of this zone it will be essential to conduct a sediment/contaminant
source study under Phase 2.
Zone 3: The primary zone of accumulation of contaminated sediment. This tide-
dominated zone is reasonably well defined by the watershed boundary, and its
restoration/mitigation is believed to be the main reason for initiating this study.


Following Figure 3, the actual zones are (approximately) delineated in Figure 4. A "close-
up" of the region very approximately covering Zones 2 and 3 is shown in the map of Figure 5. As
noted, the segment of the Lower St. Johns River (Figure 1) that measurably participates in sediment-
contaminant exchange with the zone of contaminated sediment accumulation in Zone 3 is presently
unknown (see Appendix).
Keeping the three zones in mind, based on site inspection, discussions with SJRWMD staff,
review of relevant data and literature, and modeling work described in the Appendix, we have
arrived at the following tentative conclusions:


1. While point and non-point sources of contaminants are distributed throughout the Ortega/Cedar
River watershed, the zone of primary accumulation of contaminants, due to their preferential binding









to sediments, appears to be the lower portion of the Ortega River. This situation is brought about by

the comparatively low flow velocities in this region which favor deposition of contaminated

sediment, while higher velocities in the upstream reaches of the river system favor scour, especially

during episodic (flood) events. This situation is believed to have resulted in lesser sediment

accumulation, in general, in the upper reaches of the two rivers, in comparison with the lower Ortega

River. This may not preclude the occurrence of some contaminant hot-spots in the upper reaches,

especially in the Cedar River or some of its tributaries, which appear to be the primary contaminant

source. Highest accumulation of contaminated sediment seems to be in the area of the confluence

of (lower) Ortega and Cedar Rivers.


SUB-BASINS
01000 ORTEGA RIVER
02000 FISHING CREEK
03000 BUTCHER PEN CREEK
04000 CEDAR/WILLIS BRANCH
05000 WILLIAMSON CREEK

5 km


Figure 4. Ortega/Cedar River basin, sub-basins and notional zones.
























z
I
0




Figure 5. Ortega and Cedar Rivers and contiguous
segment of the St. Johns River (main-stem).



2. Although sand bar formations and local sand bed/bank erosion have occurred in some locations,
the problem of contaminated sediment is largely restricted to fine-grained sediment that is highly
organic, and is apparently supplied significantly by the Ortega River, whose banks are wetland-
backed over significant reaches of the river.


3. Contaminants in the confluence region (PCBs and PAHs) are seemingly derived from hot-spots
(industrial areas and dump sites within the city of Jacksonville), especially in the vicinity of the
Cedar River. Some of the sources possibly remain significant, e.g., PCBs. Heavy metals and PAHs
are also likely to be derived from the marinas and docking facilities located in the lower Ortega
River, close to its mouth at the main-stem. Pesticides are likely derived from numerous non-point
sources.








4. During high river floods, part of the accumulated sediment in the lower Ortega River as well as
newly derived sediment from the upstream reaches of the river system seemingly erodes, and is
transported to the main-stem. Given the low settling velocity of this "light" sediment, it is possible
that the material is transported as far as 5 km into the main-stem beyond the mouth of the Ortega
River.


5. When high wave action and/or a storm surge occur in the main-stem, sediment is likely imported
into the lower Ortega River from the main-stem. Since this portion of the main-stem also contains
contaminated sediment, the lower Ortega River tends to accumulate this type of sediment derived
apparently from the Ortega/Cedar watershed as well as the main-stem.


6. Because synoptic and synchronous data on sediment movement and associated movement of
contaminants are presently unavailable, it is not possible to arrive at a mass budget, either for
sediment or for the associated contaminants. Given this hiatus, two key questions related to the
restoration effort, which is likely to be focused on the lower Ortega River region, remains
unanswered, namely: 1) at what rate do the contaminants arrive from the watershed and the main-
stem? and 2) at what rate are the contaminants delivered ultimately from the watershed to the main-
stem? To address these and related issues the following recommendations are made.


4.2 Task 2: Recommendation
The following project statement was developed by SJRWMD:


The purpose of this project is to develop a feasible and cost-effective approach and
work for conducting a study that will provide information needed to develop a
sediment-contaminant restoration plan for Cedar and Ortega Rivers and watersheds.
Development of the restoration plan would basically require identification of sources,
distribution and deposition of sediments, determination of sediment characteristics
and quality, assessment of the dynamics of sediment within the study area and
quantification of sediment flux to and from Cedar and Ortega Rivers.








This project may involve two phases, a planning phase (Phase 1) and an
implementation phase (Phase 2). Phase 1 will deal with preliminary investigations
and development of an efficient study approach. Phase 2 will be the actual study
phase based on the approach and work plan developed and approved in Phase 1.


The aforementioned statement appropriately defines the problem and sets out two study
phases; the first one being planning-related, and the second related to plan implementation. The
project includes restoration of the entire watershed, for which contaminant assessment will require
wide ranging technologies and expertise. It will therefore be essential to sub-divide "Phase 2" to
identifiable sub-units, both with respect to the physical domain and the work involved. "Cost-
effectiveness" is a subjective valuation that will have to be viewed, ultimately, in terms of a set of
pre-selected semi-quantitative criteria. Given the nature of the restoration problem, especially with
regard to critical accumulation of contaminated sediment in the lower Ortega River, the choice of
the entire watershed as the physical domain of the problem is appropriate.
Our recommended approach for an assessment of the sediment-contaminant problem is as
follows:


1. Analyze the problem diagnostically through mathematical modeling of the transport of
contaminants.


2. Develop a set of predictive tools, also through mathematical modeling, to assess the fate of
transported and transportable contaminants over a reasonable time period, e.g., ten years.


3. Collect necessary information on the sources/distribution of contaminants that are being
transported. Hydrodynamic, sedimentary and contaminant related data will be required. In order to
capture seasonal effects, the recommended duration of the field study is one-year. These data should
be supplemental to the data already collected or acquired by SJRWMD, and data routinely being
collected by SJRWMD and other entities (e.g., BESD). As noted later, secondary studies, if carried
out, will require additional data collection efforts and duration.








4. The specific hydrodynamic/sedimentary/contaminant data to be collected, including their temporal
and spatial distributions, is partly dictated by the hydrodynamic and sediment flux analysis carried
out in the Appendix. It should be noted, however, that in general it will be essential to address the
question of contaminant transport on a basin-wide scale. At the same time, it must be bourne in mind
that the question of addressing the restoration issue initially arose because contaminated sediment
is known to have been accumulating in the lower Ortega River, which is within a heavily utilized
residential and recreational zone adjacent (and connected) to the St. Johns River. Accordingly, the
appropriate data collection strategy is outlined under Task 3 in Section 4.3 (see also Appendix).


5. The recommended data collection and analysis is not especially of the high-risk variety, since
previously tested approaches will be used. However, as concluded in the Appendix, the presently
available data base is insufficient to enable a comprehensive determination of the extent of the
bottom contamination problem. Therefore, it will be essential to divide Phase 2 into two sub-phases -
Phase 2A covering a period of 2 years, extendable by additional 6 months, and Phase 2B for an
additional 1 year, also extendable by six additional months. In other words, the recommended
duration of Phase 2 is 3 years, extendable to a total of 4 years.


As part of the study, certain assessments of the needs for additional studies will be essential.
If the outcomes of these assessments is that these needs must be met, secondary studies will be
required. Thus, these secondary studies will be contingent upon outcomes within Phase 2.
In what follows, work plans for Zones 1, 2 and 3 are presented. The plans are strategically
grouped into those for Zones 1 and 2, Zones 2 and 3 and Zone 3. This grouping is essential due to
the overlapping character and dynamics of the three zones as defined. A caveat that applies to the
entire effort, but especially that related to the field study component, is that during the field program,
if substantial data loss occurs due to instrument breakdown or due to poor weather conditions,
additional data collection effort will be required to compensate for this loss. Since the extent of such
a loss cannot be estimated a priori, any consideration as to the time and/or additional costs that may
be incurred are excluded from further consideration in this report.








4.3 Task 3: Work Plans
4.3.1 Zones 1/2 Work Plan
SCOPE OF WORK: To assess point/non-point sources of contaminant in Ortega and Cedar Rivers,
with reference to their ultimate accumulation in the lower Ortega River and exchange with main-
stem St. Johns River.
Each of the following primary/secondary tasks should be addressed under Phase 2.


4.3.1.1 Water Level, Velocity and Stage-discharge
We recommend water level and velocity data collection at three locations shown in Figure
A.25 one each upstream Ortega River, upstream Cedar River and downstream Ortega River
(mouth). Note that the bottom-mounted pressure gage at the mouth of the Ortega River is meant to
record both tide (astronomical and storm surge) and waves. Water levels should be measured for one
year, in order to account for seasonal effects of runoff, wind and other weather-related factors. At
these flow cross-sections selective flow velocity and discharge data will be required. These can be
efficiently obtained with an Acoustic Doppler Current Profiler, or ADCP (see Section A.3.1 and
Figure A.26). These data must be used to develop stage-discharge relationships for the flow cross-
sections that are essential as boundary conditions for mathematical modeling of basin hydrodynamics
in Zone 3. Note that these relationships will inherently include inflows from all important tributaries
relevant to Zone 3. Similar relationships for the main-stem (Zone 2) are available, or can be derived
from available information. See Section 4.3.3.3 for comments concerning the use of these
relationships for predictive purposes.


4.3.1.2 Wave Data
Wave data should be collected in the main-stem off the mouth of the Ortega River for a
period of one year coincident with water level measurements. The location of the wave-pressure gage
is shown in Figure A.25. These data will be required to model the effect of storms in resuspending
contaminated sediment close to the mouth of the Ortega River (i.e., at one of the boundaries between
Zones 2 and 3). Since as noted this gage will also record the astronomical and non-astronomical
(storm surge) tides, it will serve a dual purpose.








4.3.1.3 Water Quality Sampling
We recommend weekly water sampling (phased with the tidal stage) at three locations
(Figure A.25) for one year. Large (e.g., 55 gallon) samples will be required to analyze for: 1) particle
characteristics including size, composition and TSS, 2) representative particle-bound contaminantss,
and 3) representative dissolved contaminantss. These measurements will be essential for sediment
fate modeling, as well as contaminant transport modeling. Note that depending on further
examination of modeling needs, a fourth water quality station may have to be added at one of the
interior bridges in Zone 3, although at present the time and cost of this additional effort in not
considered pending further evaluations as part of Phase 2. Similarly, it will be necessary to consider
the use of bottom sediment traps to augment the data on sediment/contaminant transport. Bottom
traps in rivers/estuaries can yield measures of net sediment deposition and associated contaminant
load. In general, their success rate varies with the sediment type, location/currents and especially the
duration over which they are sampled. See also, Section A.4.2.
Data from these stations (and test sites) must be used to calibrate/validate the selected water
quality modelss. See Sections 4.3.1.6 and 4.3.3.2 with reference to model selection. Note that while
the methodology for calibrating the hydrodynamic and sediment transport models was established
as part of the Phase 1 study (Appendix), the procedure for the calibration/validation of the water
quality model will be contingent upon the choice of the models) under Phase 2.


4.3.1.4 Sediment and Contaminant Load Rating Curves
Empirical correlations between water velocity, or bottom stress, and TSS must be developed
for all three boundary water quality sampling sites (see Section 4.3.1.3). This essentially amounts
to an improvement over the preliminary rating relations developed under Phase 1 for "normal" and
episodic conditions (Figure A.14). These correlations should serve to establish sediment flux
boundary conditions for Zone 3 required for modeling sediment fate (see Appendix). Contaminant
load rating curves analogous to sediment load rating curves must be developed for representative
particle-bound/dissolved contaminants. These curves should serve as boundary conditions for the
selected water quality model code(s). See Sections 4.3.1.6 and 4.3.3.2 with reference to model
selection.








4.3.1.5 Contaminant Source Identification
Using available information, an extensive review must be carried out of all existing point and
non-point sources of contamination. Based on this review as well as data obtained through water and
bottom sampling and bottom property mapping, a contaminant identification, location and relative
source strength plan must be developed. The basis for this plan is shown on p. 17 (box). The three
principle elements of the box are: Problem Identification, Problem Quantification, and Problem
Remediation and Plan Development. Generic options for remediation are included within the last
category. As noted in Section 4.1, Phase 2 data collection and analysis effort will be essential for
translating these options into site-specific alternatives for evaluation.
For contaminant source identification, standard remediation guidelines must be followed that
provide a sequence of assessment and feasibility investigations. Required modification of these
guidelines must be made using site-specific information. Although specific modifications cannot be
determined at this time, it will be necessary to describe them in the source identification plan to be
developed. As for guidelines, several cited sources are available including, but not limited to: U. S.
Army Corps of Engineers (1978; 1985; 1986; 1990), U. S. Environmental Protection Agency (1986)
and U. S. Army Corps of Engineers and U. S. Environmental Protection Agency (1991).


4.3.1.6 Assess Need for Basin Water Quality Modeling
Although the primary strategy for contaminant transport assessment is based on particle-
bound contaminants, it will be essential to examine the partitioning of contaminants between
sediment and water phases (Section 4.3.1.3). If the concentrations of dissolved contaminants are
found to be significant, it may become necessary to initiate an independent study of the transport of
dissolved contaminants within the entire watershed. For that purpose, additional water quality
sampling stations may have to be established in the upstream reaches of the Ortega and Cedar Rivers.
Under this task, the justification and the necessary protocol for this purpose must be developed. It
suffices to note that the data collected in this dissolved contaminant transport study should, in part,
be used to determine the fate and effect of contamination and ecological risks due to those
contaminants.
To model dissolved contaminant transport within the non-tidal zone of the watershed, if
required, our recommendation would be to survey relevant codes for application to the Ortega/Cedar
River system. One candidate is the Hydrological Simulation Program Fortran (HSPF) (Bickwell,










Plan of Action for Remediation of the Ortega and Cedar Rivers Sediments
Problem Identification
Goal: Determine ecological risks due to contamination in Ortega and Cedar Rivers sediments
Needs: Contaminant concentrations in habitat and biota
1 Assessment of problem
Historical information and personnel review
Current assessment using existing data: FDEP; RESD (formerly BESD), etc.
Report of findings and prioritization (reconnaissance report)
Preliminary sediment and tissue assessment (SJRWMD-J. Schell; RESD)
Problem Quantification
Goal: A plan for remediation of contamination in Ortega and Cedar River sediments
Needs: Volume calculations of river bottom sediment and contaminated sediment; source identification
1 Bathymetry and shoreline delineation
2 Sediment profiles and deposition areas
3 Sediment contaminants and stratigraphy
4 Hydrologic and hydrodynamic and sediment transport calculations
5 Sediment and contaminant volume calculations
6 Assessment of sources of contamination
Historic and terminated sources
Current ongoing sources
Problem Remediation and Plan Development
Goal: Approval of a plan for remediation of contamination in Ortega and Cedar River sediments
needs: Contaminant source identification, location and control; prioritization and selection of remediation
alternatives
1 Source control strategy
Point source control
Non-point source control
2 Contaminant remediation strategy
Multiple alternative project remediation plan
Must include source control
a. Leave alone
b. In-place remediation
c. Removal with off-site disposal
d. Removal with off-site contaminant remediation
e. Removal with on-site contaminant remediation
3 Permits for sediment removal will be required
ACOE; FDEP; City (if PCB contaminated sediment is transported)








et al., 1996). HSPF simulates watershed hydrology and water quality for both conventional and toxic
organic pollutants. The model incorporates a basin-scale analysis framework that includes fate and
transport in one-dimensional stream channels. It allows the integrated simulation of land and soil
contaminant runoff processes with in-stream hydraulic and sediment-chemical interactions. The
result of this simulation is a time-history of the runoff flow rate, sediment load, and contaminant
concentrations at any point in the watershed. HSPF simulates the transport of three sediment types -
sand, silt, and clay.
We recommend that a code such as HSPF be setup for the non-tidal zone, keeping in mind
the following related efforts: 1) Runoff/Extran modeling of the watershed runoff and CDM-NTS
modeling of pollutant loads carried out by Camp, Dresser & McKee, Jacksonville, 2) SWMM
modeling for storm water flows and sediment loads carried out by SJRWMD, and 3) Watershed
Assessment Model (WAM) of Soil & Water Engineering Technology, Gainesville.
With regard to the watershed level modeling, we recommend the following procedure: 1) run
the existing water quality scenario based on current TSS/contaminant sources to the rivers (especially
Cedar River), 2) run selected land use change scenarios to evaluate relative impacts on Zone 3, and
3) run selected Best Management Practice implementation scenarios to evaluate relative impacts on
the lower river system. We recommend use of existing data as well as data collected under Phase 2
for the simulations. However, as part of the assessment, it will be essential to examine the need to
set up two (or more) water quality sampling stations, in the Ortega and Cedar Rivers. These stations
would be in addition to three recommended in the lower river system (Figure A.25), and must be
well upstream of the latter.


4.3.2 Zones 2/3 Work Plan
SCOPE OF WORK: To map the sediment-bound contaminant area, and to assess sources of
sediment and contaminants exchanged between the lower Ortega and Cedar Rivers, upper Ortega
and Cedar Rivers, and the St. Johns River.
Each of the following primary/secondary tasks should be addressed under Phase 2.








4.3.2.1 Bottom Sediment Sampling
A detailed review must be carried out of available information from SJRWMD and other
entities on bottom sediment physical and geochemical properties. Based our preliminary review
carried out under Phase 1, we tentatively recommend collection of 20 bottom cores (e.g., using a
vibracorer) within the principal zone of bottom sediment accumulation in the lower Ortega River,
upstream of this zone in the Ortega and Cedar Rivers, and in the main-stem contiguous to the mouth
of the Ortega River (Fig. A.25). The cores should be analyzed for selected physical parameters,
organic sediment geochemical parameters and representative particle-bound contaminants to be
selected under Phase 2. The purpose of this analysis must be to develop maps for quantifying the
spatial (planform and vertical) distribution of contaminated sediment in Zone 3 and contiguous Zone
2. Relevant parameters to be mapped are described next in Sections 4.3.2.2, 4.3.2.3 and 4.3.2.4.


4.3.2.2 Sediment Physical Property Distribution
Carry out analysis of obtained cores including bulk and dry densities, particle size and
organic content. Develop and interpret a three-dimensional map delineating the distribution of these
parameters. Use should be made of the existing SJRWMD data base (e.g., Morgan & Eklund, 1995)
as part of the mapping process.


4.3.2.3 Organic Sediment Geochemical Property Distribution
Analyze cores for selected (e.g., two or three) relevant biogeochemical tracers in order to
qualitatively assess sources (e.g., terrigenous or marine) of sediment found in Zone 3. Potential
tracers include, e.g., sitosterol, lignin, C-N ratio, 3C-12C ratio, PAH and alkenes. Develop and
execute sediment sampling methodology. Develop a biogeochemical marker map, identify most
probable sources, and estimate relative contributions to net sediment accumulation in the lower river
basin.


4.3.2.4 Sediment-bound Contaminant Distribution
Using newly acquired bottom core information along with existing information from
SJRWMD, develop a map showing depth of organic material and contaminated upper bed zone
within Zone 3 and contiguous Zone 2.








4.3.2.5 Assess Need for Additional Coring
If the maps are found to be inadequate to fully justify the need for contaminant source and
plume assessment, especially with regard to sites in upper Ortega and Cedar Rivers and the main-
stem, a program of additional coring should be developed and executed, the data analyzed and new
information added to improve bottom sediment mapping.


4.3.2.6 Assess Need of Shallow Acoustic Bottom Profiling
If the sediment mapping in the area of major accumulation is found to be inadequate in terms
of the total thickness of contaminated sediment, the need to carry out continuous acoustic profiling
must be assessed, using equipment suitable for the very shallow depths in Zones 2 and 3. If so, a
separate study must be conducted.


4.3.2.7 Assess Need of Bioaccumulation Risk Analysis
SJRWMD and other agencies have been collecting information on bioaccumulation of
contaminants based on tissue sampling. The need to extend this analysis to examine potential risks
of ingestion of contaminants by humans and other species should be assessed, and authorized if
considered necessary. This assessment must also include costing of the study to be carried out.


4.3.2.8 Contaminant Source Assessment
Based on the sediment/contaminant load rating curves developed for the Ortega River, Cedar
River and the interface between Ortega River and the main-stem, along with the developed physical,
organic geophysical and contaminant property distribution maps, contaminant sources and relative
source strengths must be established. Accordingly, contaminant sources must be identified, located
and their relative source strengths determined following guidelines that provide for a sequence of
assessments and feasibility investigations, as described in standard remediation programs.
Modification of the standard remediation program guidelines must be made using site-specific
information. Although specific modifications cannot be determined at this time, they must be
described in the contaminant identification and location plan to be developed as described in Section
4.3.1.5.








4.3.3 Zone 3 Work Plan
SCOPE OF WORK: To assess the fate of contaminated sediment accumulated in the lower Ortega
River on a predictive basis.
Each of the following primary tasks should be addressed under Phase 2.


4.3.3.1 Sediment Transport Parameter Tests
Measurement of rates of erosion, settling velocity and consolidation of grab-sample sediment.
Rates of erosion can be measured in a Particle Entrainment Simulator or a flume, settling velocity
can be determined in a settling column, and consolidation in a consolidation column. Native water
should be used in all tests, so that the state of flocculation is not altered significantly (see, e.g., Mehta
et al., 1994; Parchure, 1980).


4.3.3.2 Sediment Code Revision
Conduct a review of numerical codes for application within the tidal Ortega/Cedar River
system. A potential candidate is the Environmental Fluid Dynamics Code (EFDC) for numerical
simulation of hydrodynamics, sediment transport and contaminant transport in the tide-driven Zone
3 (Hamrick 1992; 1996). For a comparative examination of this code in relation to other well known
codes, see Martin and McCutcheon (1999). With regard to EDFC, it should also be noted that: 1)
It has now been accepted and supported by the EPA Office of Water and Office of Research and
Development, and 2) as part of a project funded by EPA to evaluate existing water quality/sediment
transport models, Hydrogeologic, Inc. (1999) has identified EFDC as one of the seven best receiving
water quality/sediment transport models. The other six models are: CE-QUAL-ICM, CE-QUAL-
RIV1, CE-QUAL-W2, GLLVHT, HSPF and WASPS.
For the selected code, the fine sediment transport component of the code will require revision
to enable it to include state-of-the-art process modules to simulate transport of sediments found in
the Ortega/Cedar River basin. This revision can be based on, for example, the works of Jiang (1999)
and Rodriguez (2000). In addition, we advise that transport algorithms specifically meant for the
organic component of the sediment be incorporated within the selected code (see, e.g., Mehta et al.,
1997).








4.3.3.3 Contaminated Sediment Budget and Fate
Using a code such as EFDC, develop a sediment mass balance for the basin including the
contiguous main-stem domain and assess fate of sediment/contaminants with regard to exchange
between Zones 2 and 3. The general procedure for this application has been established in the
Appendix. In that context, and as noted in Section 4.3.1.4, the rating curves developed for the region
should be used as boundary conditions for running the code. The outcome of this application should
yield quantitative information on the import/export of contaminated sediment in Zone 3 in relation
to Zone 2. As a component of this analysis, it will be essential to run the model in a predictive mode
to assess, over a recommended period of 10 years, likely scenarios with regard to accumulation of
contaminants in Zone 3, and also in the contiguous Zone 2. Since such predictive scenarios are
characteristically constrained by the lack of information on future weather events, the accuracy of
prediction should be assessed, at least qualitatively. If basin-scale water quality modeling is carried
out per assessment described in Section 4.3.1.6, the results from modeling, such as through the use
of HSPF, should be incorporated in the contaminated sediment fate assessment process.
It is necessary to point out that the development of predictive scenarios on a futuristic basis
will require "extrapolation" of historic data collected by SJRWMD and other agencies and entities,
as well as data collected during the Phase 2 study. In that context, the stage-discharge relationships
to be developed under tasks described in Section 4.3.1.1, and sediment and contaminant rating
curves to be developed under tasks listed in Section 4.3.1.4, will have to be utilized. The use of these
relations as boundary conditions for the models, in conjunction with selected scenarios for future
flood events, will undoubtedly introduce increasing uncertainties with years from "present" in the
prediction of contaminated sediment loads as well as contaminant fluxes and fate. These
uncertainties must be recognized and dealt with in the best possible way when considering
restoration options.
With regard to contaminant migration, the need for a "Phase 3" work effort, that would
provide information to trace the migration of contaminants from their watershed sources to the
downstream depositional areas, is not apparent at this time. We predict that development and
implementation of a remediation plan can proceed without this migration information. A final
determination for the need for Phase 3 contaminant migration information will be required following
completion of Phase 2 work.








4.3.3.4 Restoration Alternatives Evaluation
Critically evaluate potential alternatives for basin restoration using quantitative evidence
derived from basin/main stem sediment sourcing, budget and sediment/contaminant exchanges, and
physical, geophysical and contaminant mapping (Figure 6). As part of this evaluation, information
available for SJRWMD on bioaccumulation derived from tissue samples should be utilized.



I Potential alternatives for restoration


Predictive assessment based on
rates of contaminated sediment
generation, sourcing,
accumulation and transport



Recommendations concerning
the alternatives


Figure 6 Assessment process for potential restoration
alternatives.


Further information on bioaccumulation may become available depending on the need and
execution of an additional investigation per Section 4.3.2.7.
As noted in Table 2, the final restoration evaluation task must be carried out towards the end
of the Phase 2 study. However, it is recommended that based on the field data analysis effort during
the first year of the study, a set of site-specific remediation options be developed on a very
preliminary basis at the end of the Task 4.3.1.6, i.e., at the end of 1.5 years in to the Phase 2 study.
The evaluation will allow establishing and prioritizing potential restoration alternatives for
the Ortega/Cedar River watershed. Selection of the restoration alternatives will provide the necessary
information that will be used to guide the planning of investigations needed to develop the final
remediation plan. This evaluation and prioritization process must follow standard remediation
program guidelines, and modifications must be made using site-specific information. Although








specific modifications cannot be determined at this time, they must be described in the remediation
plan-of-action and remediation to be developed as described in Section 4.3.1.5.


Table 1. Task numbers and titles
Task No. Task Title

4.3.1.1 Water Level, Velocity and Stage-discharge

4.3.1.2 Wave Data

4.3.1.3 Water Quality Sampling

4.3.1.4 Sediment and Contaminant Load Rating Curves

4.3.1.5 Contaminant Source Identification

4.3.1.6 Assess Need for Basin-scale Water Quality Modeling

4.3.2.1 Bottom Sediment Sampling

4.3.2.2 Sediment Physical Property Distribution

4.3.2.3 Organic Sediment Geochemical Property Distribution

4.3.2.4 Sediment-bound Contaminant Distribution

4.3.2.5 Assess Need for Additional Coring

4.3.2.6 Assess Need of Shallow Acoustic Bottom Profiling

4.3.2.7 Assess Need for Bioaccumulation Risk Analysis

4.3.2.8 Contaminant Source Assessment

4.3.3.1 Sediment Transport Parameter Tests
4.3.3.2 Sediment Code Revision

4.3.3.3 Contaminated Sediment Budget and Fate

4.3.3.4 Restoration Alternatives Evaluation


4.4 Task 4: Report
The above recommendations constitute the main features of this (Phase 1) report. References
cited within the text, and in the Appendix, are included following the Appendix. With regard to the
implementation of the recommendations under Phase 2, the following paragraphs should be noted.












Table 2. Task numbers, durations and costs


Cost is Irt iasstssIIlent stUly only. I mil stuuy is require, cost womud be on me order of o,4tu,00; uurauion z months.
b Cost is for assessment study only. If full study is required, cost would be on the order of $50,000; duration 4 months.
'Cost is for assessment study only. If full study is required, cost would be no the order of $45,000; duration 3 months.

d Cost is for assessment study only. If full study is required, cost would be on the order of $40,000; duration 6 months.



The evaluation of the problem, as reported, is contingent upon three factors: 1) the project

statement, in particular related to "feasible and cost-effective approach and work for conducting a

study that will provide information needed to develop a sediment contaminant restoration plan for

Cedar and Ortega Rivers and watersheds", 2) initial and subsequent discussions with SJRWMD staff

regarding the region of heavy emphasis where restoration is a critical issue, namely the lower Ortega

River (including the lower Cedar River) and the contiguous waters of the St. Johns River (i.e., main-


Task no. Month Cost ($)

Phase 2A Phase 2B

1 2 3 4 5 6 7 8 9 1 1 1 1 2 3 4 5 6 7 8 9 1 1 1 1 2 3 4 5 6 7 8 9 1 1 1
1 2 012 01 2

43.1.1 x x x x x x x x 49,100

43.1.2 x x x x x x x 22,300

43.13 x x x x x x x x 64,200

4.3.1.4 x x 13,800

43.1.5 x x x 43,000

43.1.6 x x 7,200a

4.3.2.1 x x 58,150

43.2.2 x x x 7,500

43.23 x x x x 25,910

43.2.4 x x 6,910

4.3.2.5 x x 7,250b

43.2.6 x x 7,510c

43.2.7 x x 7,270d

4,3.2.8 x x x 6,750

43.3.1 x x x 13,700

43.3.2 x x 13,350

4.3.33 x x x 16,600

4.3.3.4 x x 28,750
a C .-- :. .. ..- -.-.. -1._. re -1 U -... ----i ------ .....111-- ^-- ----- _lU Ar\" -i...U- 1 ----I








stem), and 3) the directive by SJRWMD staff to develop a plan independent of any potential
participation in Phase 2 by SJRWMD.
A point of emphasis is the recognition that despite the availability of some data on river
runoff and water levels, bathymetry, bottom sediment composition, bottom contaminant distribution
and water quality (especially with regard to bacteriological contamination), development of a
comprehensive field data set required to meet the objectives per project statement is critically
important. As a result, certain assessments (see Tables 1 and 2) will be required as part of the Phase
2A study, in order to complete the study by the end of Phase 2B. These assessments may require
additional studies which presently can be defined only in qualitative terms. Such studies would
essentially be secondary studies in our interpretation. Costs for the same can only be determined
once they are defined quantitatively under Phase 2A. Finally, it should be noted that the costs
included in Table 2 are estimates and, further, this report does not constitute a formal proposal for
further work under Phase 2 by the University of Florida.
Table 2 does not itemize time for report writing. However, written, quarterly progress reports
and a final report for the entire study should be expected. The progress report at the end of Phase 2A
should summarize the findings up to that point in time. The final report should be comprehensive.


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Gainesville.








Keller, A. E., and Schell, J. D. (1993). Lower St. Johns River basin reconnaissance report volume
5 sediment characteristics and quality. Technical Publication SJ93-6, St. Johns River Water
Management District, Palatka, FL.
Land, J. M., Kirby, R., and Massey, J. B., 1997. Developments in the combined use of acoustic
doppler current profilers and profiling siltmeters for suspended solids monitoring. In:
Cohesive Sediments, N. Burt, R. Parker and J. Watts eds., John Wiley, Chichester, UK, 187-
196.
Li, Y., Mehta, A. J., Hatfield, K., and Dortch, M. S. (1997). Modulation of constituent release across
the mud-water interface by water waves. Water Resources Research, 33(6), 1409-1418.
Martin, J. L., and McCutcheon, S. C. (1999). Hydrodynamics and Transport for Water Quality
Modeling. CRC Press, Boca Raton, FL.
Mehta A. J. (1988). Laboratory studies on cohesive sediment deposition and erosion. In: Physical
Processes in Estuaries, J. Dronkers and W. van Leussen eds., Springer-Verlag, Berlin, 427-
445.
Mehta, A. J., Lee, S.-C., Li, Y., Vinzon, S. B., and Abreu, M. G. (1994). Analyses of some
sedimentary properties and erodibility characteristics of bottom sediments from the Rodman
Reservoir, Florida. Report UFL/COEL/MP-94/03, Coastal and Oceanographic Engineering
Department, University of Florida, Gainesville.
Mehta, A. J., Kirby, R., Stuck, J. D., Jiang, J., and Parchure, T. M. (1997). Erodibility of organic-
rich sediments: A Florida perspective. Report UFL/COEUMP-97/01, Coastal and
Oceanographic Engineering Department, University of Florida, Gainesville.
Mehta, A. J., and Li, Y. (1999). Principles and process-modeling of cohesive sediment transport.
OCP 6297 Lectures, University of Florida, Gainesville.
Morgan & Eklund, Inc. (1995). Investigations of water depth and sediment characteristics, Ortega
River and Cedar Creek, Duval County, Florida. Project Report, Wabasso, FL.
Netzband, A., Gonnert, G., and Christiansen, H., 1999. Water injection dredging in Hamburg -
application and research. Proceedings of CEDA Dredging Days'99, Central Dredging
Association, Amsterdam, The Netherlands.
Parchure, T. M. (1980). Effect of bed shear stress on the erosional characteristics of kaolinite. M.S.
Thesis, University of Florida, Gainesville.








Rodriguez, H. N. (2000). Mud bottom evolution at open coasts. Ph. D. thesis, University of Florida,
Gainesville, FL, 256p.
Teeter, A. M., Letter, J. V., Pratt, T. C., Callegan, C. J., and Boyt, W. L. (1996). San Francisco Bay
long-term management strategy (LTMS) for dredging and disposal, report 2, baywide
suspended sediment transport modeling, Technical Report HL-96-8, U. S. Army Engineer
Waterways Experiment Station, Vicksburg, MS.
Tetra Tech, Inc. (1999). EFDC Technical Memorandum Theoretical and Computational Aspects
of Sediment Transport in the EFDC Model. Project Report, Fairfax, VA.
Towner, J. V. (1994). Contaminants in estuarine sediments. In: Coastal, Estuarial and Harbour
Engineer's Reference Book, M. B. Abbott and W. A. Price eds., Chapman & Hall, London,
585-596.
U.S. Army Corps of Engineers (1978). Treatment of contaminated dredge material. Technical Report
DS-78-14, U.S. Army Engineer Waterways Experiment Station, Vicksburg, MS, 46p.
U.S. Army Corps of Engineers (1984). Shore Protection Manual. U.S. Army Engineer Waterways
Experiment Station, Vicksburg, MS.
U.S. Army Corps of Engineers (1985). Management strategy for disposal of dredged material:
Contaminant testing and controls. Miscellaneous Paper D-85-1, U.S. Army Engineer
Waterways Experiment Station, Vicksburg, MS, 40p.
U.S. Army Corps of Engineers (1986). Guidelines for selecting control and treatment options for
contaminated dredged material requiring restrictions. Puget Sound Dredged Disposal
Analysis Reports, U.S. Army Engineer Waterways Experiment Station, Vicksburg, MS,
480p + appendices.
U.S. Army Corps of Engineers (1990). Review of removal containment and treatment technologies
for remediation of contaminated sediment in the Great Lakes. Miscellaneous Paper EL-990-
25, U.S. Army Engineer Waterways Experiment Station, Vicksburg, MS, 119p + appendices.
U.S. Army Corps of Engineers (1995). Willis Branch Jacksonville, Florida Final Detailed Project
Report and Environmental Assessment. Section 205 Flood Control, Jacksonville, FL.
U.S. Environmental Protection Agency (1986). Ecological Risk Assessment. Hazard Evaluation
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Washington, DC.








U.S. Environmental Protection Agency and the U.S. Army Corps of Engineers (1991). Evaluation
of dredged material proposed for ocean disposal testing manual. U.S. EPA and U.S. Army
Corps of Engineers, Washington DC, 200p +appendices.








APPENDIX: A PRELIMINARY ASSESSMENT OF THE EFFECT OF EPISODIC
EVENTS ON SEDIMENT YIELD IN ZONE 3 AREA OF SIGNIFICANT
ACCUMULATION OF CONTAMINATED SEDIMENT


A.1 Introduction
In order to make a preliminary assessment of contaminated sediment budget for Zone 3 (i.e.,
the downstream region of the Ortega/Cedar River basin, where significant accumulation of
contaminated sediment has occurred) and its inter-relationship with Zones 1 and 2, a preliminary
hydrodynamic and sediment transport modeling study was carried out under Phase 1, mostly using
available data on water levels, discharges, currents, bottom cores and suspended solids. Grab
sediment samples were additionally collected to determine sedimentary parameters relevant to their
erosion and settling properties. An inspection of the region along with analyses of the collected
sediment samples as well as data and information supplied by SJRWMD indicated that the problem
of contaminants is associated with the fine-grained component of suspended sediment which
predominates the zone. Localized, submerged sand bars exist within the basin, but their role in
transport of contaminants is likely to be minimal. In connection with basin restoration related issues,
the questions that require answers are:
1) Where does the sediment in the accumulation zone come from?
2) Is any sediment exported to the main-stem?
3) With regard to sediment accumulation, what is the role of episodic factors, both with respect to
runoff via the Ortega/Cedar River watershed and resuspension/transport due to wave/storm surge
action in the main-stem?
4) Is the data base sufficient and accurate enough to enable prediction of the fate of contaminated
sediment, and if not, what additional data must be collected?
The assessment to address the above questions was based mainly on the application of two
three-dimensional numerical codes Coastal and Estuarine Hydrodynamics Model COHYD-UF,
and Coastal and Estuarine Cohesive Sediment Model COSED-UF developed at the University of
Florida (Jiang, 1999).
In what follows, applications of the above models and results therefrom are summarized.
Data supplied by SJRWMD on submerged bathymetry, water level variations, river discharges,








current speeds, TSS (total suspended solids), bottom core descriptions and core-based sediment
accumulation rates were used along with analyses of additional data derived from field sampling of
bottom sediment carried out during Phase 1.


A.2 River Flow Dynamics
COHYD-UF is a three-dimensional hydrodynamic code based on a finite-difference
schematization of the governing equations of flow momentum and continuity. The coordinate
scheme is rectilinear; the vertical coordinate is a-transformed for improving the versatility of vertical
profile simulations. For Zone 3 the model grid (60 m x 60 m in horizontal dimensions) is shown in
Figure A.1. Typical depths in the Ortega River mouth area are 2 to 2.7 m (below mean low water),
and in the area of confluence of the two rivers, where significant accumulation of contaminated
sediment has occurred, the depths are only on the order of 1.2 m. In the upper reaches of the two
rivers within Zone 3 and in Zone 2, the depths are greater at several locations, especially in the
Ortega River, where a comparatively deep (as much as 5 m) channel occurs. This channel is an
indicator of the scour potential of river discharge during high river runoff events.
For the model grid, the vertical water column was sub-divided into 10 layers. Since exchange
of sediment between Zone 3 and the main-stem (Zone 2) is an important issue, the main-stem
segment between Fuller Warren Bridge and Buckman Bridge was also modeled. Note that given the
potential for down-river contamination from the Ortega/Cedar Rivers into the main-stem, in future
it may be essential to extend the modeling effort up to (and possibly beyond) Main Street Bridge,
eastward of Fuller Warren Bridge (see Figure 2). In any event, the 400 m x 400 m grid for the
presently modeled domain is shown in Figure A.2. In this case the water column was sub-divided
into 5 layers. This domain also includes Zone 3 using the same coarse grid. Based on data supplied
by SJRWMD, model input parameters were selected as follows.
For both modeled domains, the characteristic bottom roughness height was selected (by
calibration against flow data) to be 0.5 mm. River runoff and (semi-diurnal) tidal range at the open
boundaries of the model were specified per Table A.1. These runoffs are derived from data obtained
by SJRWMD during the 1997-98 period. The maximum value represents El Nifio related outflow
in 1998. Also included in the table is a nominally representative storm surge at the mouth of the
Ortega River. There are two possible modes by which storm surge of this magnitude can occur; one






Ortega River Mouth


N

\


Cedar River




Butcher Pen


0 600 m


Figure A. 1 Numerical fine mesh grid for the Ortega and Cedar Rivers,
Zone 3.


Fuller Warren Bridge


Buckman Bridge


Figure A.2 Numerical coarse mesh grid for the main-stem (part of Zone 2) and Zone 3.








is due to the propagation of a coastal storm surge at Mayport up St. Johns River. Another possibility
is wind induced surge within the Lower St. Johns River. At the mouth of the Ortega River, a 6 km
long wind fetch occurs for wind blowing from the south over the wide stretch of the St. Johns River
in this region. The mean water depth along this fetch is 2.1 m.


Table A. 1 River runoff, tidal range and storm surge at the modeled domain boundaries
Location River runoff Tidal Storm
(m3/s) range surge
Annual Maximumb () (
meana

Upstream Ortega River 5.0 205 0.36 -d

Upstream Cedar River 4.5 102 0.38

Upstream Fishing Creek 1.1 27 -

Upstream Butcher Pen Creek 0.3 6 -

Downstream Ortega River (mouth) 0.43 0.43e

Fuller Warren Bridge 0.50

Buckman Bridge 50 2,075 0.30
a From 1997/98 stream gaging data.
b 1998 El Nifio based values.
C For spring tide.
d Not specified.
e Corresponds to an "extreme" wind speed of 87 km/hr.

In addition to the runoff conditions given in Table A.1, flow simulations were also carried
out with zero river runoffs, i.e., solely tide-driven water transport in the rivers during the dry period.
Since the (annual) mean runoffs are quite low, the results were not significantly different from those
obtained with zero runoffs. Thus, zero runoff results are not presented in what follows.
Figures A.3 through A.7 show peak velocity vectors in Zone 3. In Table A.2, near-bottom
velocities are reported at five stations indicated in Figure A.8. Based on these figures and table, the
following relevant observations are derived:
1) Under mean runoff conditions the flow in the region is largely tide-driven, with velocities (and
associated bed shear stresses) that are too low to cause bottom sediment resuspension (Mehta, 1988).
Since, however, suspended sediment concentrations during non-episodic conditions tend to be very


A-4








N

\


0 600 m


Cedar River


50 cm/s


Figure A.3 Simulated peak ebb flow velocity vectors at mean river runoff
condition in Zone 3.


Ortega River Mouth
N

t 0 600 m





Cedar River .. _- .1

Ortega River

50 cm/s







Figure A.4 Simulated peak flood flow velocity vectors at mean river runoff
condition in Zone 3.









N
\


0 600 m


Cedar River


100 cm/s


Figure A.5 Simulated peak ebb flow velocity vectors at maximum river runoff
condition in Zone 3.

Ortega River Mouth
N "1 1


fill 0 600 m






Cedar River '

Ortega River

100 cm/s







Figure A.6 Simulated peak flood flow velocity vectors at maximum river
runoff condition in Zone 3.


A-6







Ortega River Mouth
N

0 600 m



IZ i



Cedar River .


Otegar River


2 cm/s






Figure A.7 Simulated Lagrangian residual current velocity vectors at
mean river runoff condition in Zone 3.











6




2 E
3
S






500 0 500 1000 Meters
5


Figure A.8 Sites for simulated peak velocities near the
bottom reported in Table A.2.


A-7








Table A.2 Peak ebb and flood near-bottom velocities at selected sites in Zone 3
Site Peak velocity at mean river Peak velocity at maximum
runoff river runoff
(m/s) (m/s)
Ebb Flood Ebb Flood
1 (Ortega River mouth) 0.18 0.17 0.40 -a
2 (Ortega River near confluence) 0.13 0.11 0.46 -
3 (Ortega River near confluence) 0.16 0.14 0.32 -
4 (Cedar River near confluence) 0.16 0.15 0.38 -
5 (Upstream Ortega River) 0.12 0.10 0.32 -
6 (Upstream Cedar River) 0.11 0.10 0.21
a Flow was ebbing.


low (-5-20 mg/L), deposition is likely to be low as well. It should be noted that the Ortega River
provides the larger runoff of the two rivers, and because it is a relatively significant source of
organic-rich sediment, this river is likely to be the main contributor to deposition in the area of the
confluence of the river with Cedar River.


2) During maximum river runoff conditions, the flow field within Zone 3 is overwhelmingly
determined by runoff, so that even during rising tide in the main-stem, the flow continues to ebb.
High velocities sufficient to scour the bottom occur (Mehta, 1988). At the same time, because
suspended sediment concentrations tend to be high (-50 mg/L and higher), deposition is likely to
occur in areas where current velocities are comparatively low. It appears that the high velocities keep
the rivers "clean" by preventing deposition in the upstream areas, an evidence of which is the deep
channelized cross-section of the Ortega River upstream of Timuquana Bridge (located approximately
5 km upstream of the mouth of the Ortega). Downstream of the confluence, the river reach closer
to its north bank is amenable to deposition because of the presence of marinas, which tend to slow
the current. In contrast, the flow along the south bank is comparatively unhindered, and potentially
eroding at times of high outflows.


3) Flow circulation cells occur within the region. Three cells, one in Ortega River upstream of Cedar
River, one in Cedar River and one in Ortega River downstream of Cedar River, are observed in
Figure A.7, wherein these cells are represented in terms of Lagrangian (tide-mean) residual current


A-8








vectors. These cells are not found under conditions of maximum runoff, when the flow is strongly
directed downstream at all points within the system. It is not certain exactly how these gyres
influence the sediment transport regime. For suspended fine sediments they could act to trap
sediment which would deposit. High accumulation of sediment in the general area can be cited as
corroborative evidence.


Figures A.9 through A. 12 show peak velocity vectors in the main-stem along with those in
Zone 3 for mean and maximum runoff conditions in the Ortega/Cedar Rivers. Peak velocities at sites
shown in Figure A.13 are given in Table A.3. Based on the observed flow field patterns the
following conclusions can be drawn:


1) Under mean flow conditions, the flow in the main-stem is likely to be mainly depositional, with
peak velocities barely reaching levels (e.g., 0.30 m/s) at which some resuspension of bottom material
likely occurs.


2) At maximum runoff conditions in the Ortega/Cedar basin coupled with the St. Johns River, peak
flow velocities are conducive to resuspension and, furthermore, outflow velocities from the
Ortega/Cedar River system are strong and directed towards Fuller Warren Bridge. This means that,
provided a high rate of sediment discharge occurs from Zone 3, the debouched material may be
transported several kilometers north of the mouth of the Ortega River. This situation may be
exacerbated by the observed direction of flow in the main-stem, which is northward even during the
rising tide under maximum runoff conditions in the main-stem (Figure A.12).


A.3 Sediment Fluxes
The primary objective in simulating the flow field was to model fine sediment transport. For
that purpose, COSED-UF, which is linked to COHYD-UF, was applied. Details of this code and its
validation have been documented fully in Jiang (1999). Application to assess sediment fluxes in
Zone 3 is summarized in the following sections.


A-9











N





'- tt t 50 cm/s


.\\ \
I X\',N \\\\ N





0 2km I f







Figure A.9 Simulated peak ebb flow velocity vectors at mean runoff
condition in the main-stem and Zone 3.


N





50 cm/s






0 2km \ \\











Figure A.10 Simulated peak flood flow velocity vectors at mean runoff
condition in the main-stem and Zone 3.
0 2 km Ji i ; ,

/ I i, d I I c
. . ,' / I I I I 1


A-10




















I fU 50 cm/s







I rl It ltl p t-
-.r I- o / / It .-
N N N \ \ \ |




S 2kin / r I / I ,
0 2km 'ifitir







Figure A. 11 Simulated peak ebb flow velocity vectors at maximum runoff in
the main-stem and Zone 3.


Figure A. 12 Simulated peak flood flow velocity vectors at maximum runoff
condition in the main-stem and Zone 3.


A-11






























Figure A. 13 Sites for output of simulated maximum velocities near the bottom
in the main-stem.


Table A.3 Peak ebb and flood near-bottom velocities at selected sites in the main-stem
Site Peak velocity at mean Peak velocity at maximum
runoff condition in the runoff condition in the
main-stem and Zone 3 main-stem and Zone 3
(m/s) (m/s)

Ebb Flood Ebb Flood

1 (North of Ortega River mouth) 0.30 0.34 0.43 a

2 (Off Ortega River mouth) 0.22 0.21 0.32

3 (South of Ortega River mouth) 0.22 0.22 0.28

4 (South of Ortega River mouth) 0.21 0.21 0.26

5 (South of Ortega River mouth) 0.19 0.19 0.24
a Flow was ebbing.


A-12








A.3.1 Open Flow Boundary Condition Specification
Using data on flow velocities and TSS concentrations at or near the flow boundaries (Figure
A.1), along with simulations of flow velocities at times corresponding to periods at which TSS
concentrations were determined, the resulting sediment rating curves are shown in Figure A. 14. The
lower curve relates TSS to flow-induced bottom shear stress during flows in the system due to river
runoff and tide. This curve was applied to all the open boundaries for simulations of TSS and bottom
deposition throughout Zone 3, with the exception of conditions when wave action is significant.
Waves can enhance current induced resuspension in two ways: 1) by increasing the bed shear
stress, and 2) by fluidizingg" the bed under cyclic (wave) loading. Inasmuch as fluidization loosens
the bed by reducing its shear strength, at a given applied fluid stress the mass of sediment eroded per
unit time is greater than what occurs in the absence of fluidization. As a result, the TSS-bed shear
stress rating curve is different for a bed subjected to tidal flow, than for a bed fluidized by waves
(Figure A.14).
When waves occur, they tend to resuspend sediment mainly in the main-stem, since within
Zone 3 the fetches are too limited to generate high waves. Hence, for examining sediment fluxes in
Zone 3, the rating curve inclusive of wave effect in Figure A.15 was applied to the open boundary
at the mouth of the Ortega River, while the lower curve was used for the other flow boundaries. The
effect of waves in enhancing TSS transport is as follows.
As noted, the maximum wind fetch is 6 km along the southern direction from the mouth.
Assuming a wind speed of 64 km/hr along this fetch, the wave height and period in 1.2 m water
depth near the mouth are found to be 0.55 m and 3 s, respectively (U.S. Army Corps of Engineers,
1984). These wave conditions (along with typical parameters representing the erodibility and settling
of sediment given in Table A.4 and discussed later) can be used to solve for the time evolution of
the suspended sediment concentration (or TSS) using a model for the vertical transport of fine
sediment (Mehta and Li, 1999). The assumed initial condition is zero TSS in the water column.
Under continued wave action (and a selected mean tidal current of 0.3 m/s), the final concentration
profile is observed to generate a TSS (concentration) of 88 kg/m3 (or mg/1), which is about four times
greater than what would occur under a 0.3 m/s current alone. This comparatively high TSS can be
further enhanced if a wind-induced water level surge occurs. As indicated in Table A.1, the effect
of a 0.43 m surge coupled with waves near the mouth of the Ortega river was examined with
reference to sediment transport in Zone 3, and is described later.


A-13











60



50



40



o

0



20
lOt o

o



0 0.05 0.1 0.15 0.2
Bottom shear stress (Pa)


0.25 0.3 0.35


Figure A. 14 Sediment rating curves TSS as a function of bottom shear
stress. Circles are based on data.


Final Profile




- - - --






- - - - - ---
t1


*\\ \
--.. ---v.iA- -


. . . . - - - -.


Suspended Sediment Conc. (kg/m3)


Figure A. 15 Resuspension due to 0.55 m high and 3 s period waves at the mouth of
the Ortega River. The plot shows suspended sediment concentration profile evolution
with time, starting with zero initial concentration.





A-14


i'-i
S.-



--. .


Z.. .. . .


U








Table A.4 Bottom sediment data: densities, organic content, erosion rate constant and settling
velocity
Sample number Bulk Granular Organic Bed shear Erosion rate Settling
density density content strength, r, constant, Em velocity
(kg/m3) (kg/m3) (%) (Pa) (kg/m2sPa) (m/s)
UF99ME39B 1166 a 15.0 0.105 9.87x10-4

UF99ME10B 1260 1037 19.8 0.070 3.57x10-5 2.9x104

UF99ME4B 1030 1286 25.1 0.106 7.89x104 3.6x104

UF99ME4A 1067 1970 0.112 1.21x104

UF99ME20A 1145 22.7 0.127 9.09x10"

UF99ME21F 1007 1055 35.9 -2.9x10-4

UF99ME18A 1037 25.4 -

Representative 1102 1437 24.0 0.107 7.32X10-4 3.1X10-4
values
a Not measured.


A.3.2 Bottom Boundary Condition Specification
Grab samples of bottom sediment collected at sites indicated in Figure A. 16 were subjected
to laboratory analyses for relevant sediment bed properties and sediment transport dependent
parameters. The methods used for these analyses are given in Mehta et al. (1997). The properties
include: (wet) bulk density, particulate (or granular) density and organic content (loss on ignition).
Transport related parameters include: bed shear strength (with respect to erosion), erosion rate
constant and the settling velocity. These values from the sites as well as representative values chosen
for use in COSED-UF are given in Table A.4.


The shear strength and the erosion rate constant in Table A.4 refer to the following equation:


E = Em(tb T)


(A.1)


where e is the rate of bottom sediment erosion (mass eroded per unit bed area per unit time), em is
the erosion rate constant, Tb is the bed shear stress and r, is the bed erosion shear strength. The bed


A-15








shear stress is generated by COHYD-UF, and Eq. A.1 calculates e in COSED-UF. Laboratory
determined erosion rate data from five of the seven sites are given in Figures A. 17 through A.21. Of
the remaining two, UF99ME21F was tested for physical properties and settling velocity, whereas
UF99ME18A was tested for bulk density and organic content. Figure A.22 shows a cumulative plot
based on erosion data from all five sites. Note that from each erosion plot, the shear strength is
obtained as the intercept of the line on the horizontal axis, and the erosion rate constant is equal to
the slope of the line (see, e.g., Figure A.17). As a result of the general similarity of all sediment
samples with regard to the resuspension potential, the data points in Figure A.22 exhibit consistency
in terms of a unified trend.


Figure A. 16 Sites of collection of bottom sediment grab
samples.


A-16












x 10"s


Sample 39B


3.5



3



2.5

c.J





C
i 2






TS
0.5-
0

0.5 -




0 0.05 0.1
Shear stress (Pa)


Figure A.17 Bottom erosion rate data: Sample 39B.


x 10-
xl10


Sample 10B


c" 1.2





cr 0.8
c
0

w
0.6 -


0.4 -


0.2


0
0 0.02 0.04 0.06 0.08
Shear stress (Pa)


Figure A.18 Bottom erosion rate data: Sample 10B.


0.1 0.12


A-17











x 10,5


Sample 4B


'2 -
CY
E



a
r

21


/O
w




00


0 0.05 0.1 0.15
Shear Stress (Pa)

Figure A. 19 Bottom erosion rate data: Sample 4B.


x 10o5 Sample 4A
4





3





.2

0
/











0
0 0.05 0.1 0.15
Shear stress (Pa)

Figure A.20 Bottom erosion rate data: Sample 4A.
Figure A.20 Bottom erosion rate data: Sample 4A.


A-18












x 10.5
2









CY
E




0





-
w








0


Sample 20A


0 0.05 0.1
Shear Stress (Pa)


Figure A.21 Bottom erosion rate data: Sample 20A.


x 10"5
4






3




0,r
E


02

c

2
w


Cummulative Plot


0 0.02 0.04 0.06 0.08 0.1
Shear stress (Pa)


Figure A.22 Cumulative bottom erosion rate data.


0.12 0.14 0.16


A-19








A.3.3 Sediment Flux and Yield Simulations
COSED-UF (in conjunction with COHYD-UF) was used to simulate bottom deposition at
selected sites where annual mean deposition rates were determined by SJRWMD from analyses of
bottom cores (Donoghue, 1999). Sites of these cores are shown in Figure A.23. In Table A.5, model
simulated rates are compared with measured rates. Observe that there is an order of magnitude
agreement between measurements and simulations. The simulations are based on the following
weighted rate, Ah, obtained from the corresponding rates Ahmean and Ahmax under mean and
maximum runoff conditions, respectively:


Ah = 363Ahmea + 2Ahmax


The reason for this weighting is that, assuming the supply of sediment in the area of its deposition
is from the Ortega and Cedar Rivers (as opposed to the main-stem), deposition under mean runoff
conditions alone cannot account for what is measured it is essential to add 2 days of deposition






A 32








27A

3 29





500 0 500 1000 Meters


Figure A.23 Sites of bottom sediment accumulation rate data.


A-20


(A.2)








Table A.5 Measured and simulated sedimentation rates
Site Measured rate Simulated rate
(cm/yr) (cm/yr)

15 (Ortega) 19.6 27.9
25 (Ortega) 18.8 8.1

27 (Cedar mouth) 19.4 23.8

35 (Ortega) 4.9 19.8

29 (Ortega) 1.3 2.5

24 (Ortega) 4.5 6.6
8 (Ortega) 4.3 10.6

32 (Ortega mouth) 7.6 -b
a From Donoghue (1999)
b Site was outside modeled (Zone 3) domain.


under maximum runoff to 363 days of deposition under mean runoff to obtain the total annual rate
of sedimentation. The significance of this finding is that synoptic data on runoffs and TSS covering
"normal" as well as episodic conditions are required for an accurate simulation of sedimentation in
Zone 3. However, as described next, it will be essential to extend the data collection effort into Zone
2, especially within the contiguous domain of the main-stem, in order to develop a sediment budget,
hence a predictive capability in terms of the fate of contaminated sediment.
Observe the high rates of accumulation at sites 15, 25 and 27, all located close to the northern
bank of the Ortega. It is believed that two causes contribute to sedimentation there the relatively
low currents associated with Cedar River, and effective flow resistance due to marinas and moored
vessels. In contrast, low accumulations at sites 8 and 29 closer to the southern bank of the Ortega
are likely to be due to the erosion potential of the Ortega during high runoff. Velocity vectors in
Figure A.3 are qualitatively in agreement with these observations. If indeed erosion does occur, one
can expect the material to be exported to the main-stem during episodic runoff conditions, largely
by the high discharge and associated velocities in the Ortega. Also, given the higher load of sediment
derived from the Ortega in comparison with the Cedar, it appears that the downstream sedimentary
regime of Zone 3 is controlled mainly by the Ortega. Thus, while the Cedar is believed to be the
main supplier of contaminants to Zone 3, sediment is mainly supplied by Ortega. As a result,


A-21








sorption and binding of contaminants by sediment is likely to occur actively within the lower reaches
of the Ortega.
Sediment transport yields in metric tons per day (1 ton = 1,000 kg) calculated by COSED-UF
at six cross-sections within Zone 3 (shown in Figure A.24) are given in Table A.6. Observe that at
the mean runoff condition the yields at ebb and flood are such that the net values are low (compared
to gross values). For example, at Section 1 (Ortega River mouth) the yield over ebb is 74.4 tons/d
and over flood it is 69.0 tons/d. The net, 5.4 tons/d, is out of Zone 3 and into the main-stem. In
contrast to this low net yield, at the maximum runoff condition the net increases to 64.7 tons/d,
because in that case sediment is exported to the main-stem over the entire tidal cycle. The fact that
the lower reach of the Ortega is known to be a net recipient of sediment, even as large sediment
export occurs out of Zone 3 during episodic runoff, suggests that sediment supply from the main-
stem may not be negligible under certain conditions. Since under normal tides the ebb and flood
yields tend to approximately balance at the Ortega River mouth, the role of episodic conditions in
the main-stem for sediment import into Zone 3 is a natural issue for further examination, as
described next.


Table A.6 Calculated sediment yield at selected cross-sections in Zone 3
Section Yield at mean runoff Yield at maximum runoff
(tons/d) (tons/d)

Ebb Flood Net Ebb Flood Net

1 (Ortega mouth) 74.4 69.0 5.4 (ebb) 64.7 64.7 (ebb)

2 (Confluence) 61.9 56.8 5.1 (ebb) 57.4 57.4 (ebb)

3 (Confluence) 28.0 22.1 5.9 (ebb) 25.7 25.7 (ebb)

4 (Confluence) 23.4 18.1 5.3 (ebb) 21.6 21.6 (ebb)

5 (Up-Ortega) 14.8 9.2 5.6 (ebb) 12.8 12.8 (ebb)

6 (Up-Cedar) 18.2 14.1 4.1 (ebb) 17.2 17.2 (ebb)


In Table A.7, sediment yields (in metric tons per day) are calculated at the cross-sections of
Figure A.24 under two episodic conditions in the main-stem: 1) wave action due to an assumed 64
km/hr wind (see Section A.2.1), and 2) an assumed 0.43 m storm surge in addition to a 0.43 m tide
(Table A.1). When waves occur in the main-stem, as a result of resuspension during flood a


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considerable quantity of sediment can enter Zone 3 at Section 1 (Ortega River mouth). As shown in
Table A.7, the net import would be 46.4 tons/d. If storm surge were added the net would rise, by an
order of magnitude, to 376.0 tons/d.
Since two critical issues related to the restoration effort for the lower reach of the Ortega
River are: 1) the rate (if any) at which contaminated sediment is exported to the main-stem from
Zone 3, and 2) the corresponding rate at which sediment (especially contaminated) is imported into
Zone 3 from the main-stem, the summary provided in Table A.8 sheds light on transport related
questions that must be answered as a basis for assessing restoration options. Note that "Normal"
corresponds to mean runoff condition, and "Extreme river runoff" corresponds to the maximum
runoff condition. Data for the Ortega are from yields at cross-section 5 in Table A.7, for the Cedar
at cross-section 6, and from the main-stem at cross-section 1.


Table A.7 Calculated sediment yield at selected cross-sections in Zone 3 under mean runoff along
with waves and storm surge in the main-stem
Section Yield with waves in main-stem Yield with waves and storm surge
(tons/d) in main-stem
(tons/d)
Ebb Flood Net Ebb Flood Net

1 (Ortega mouth) 58.6 105.0 46.4 (flood) 133.0 509.0 376.0 (flood)

2 (Confluence) 33.4 36.4 3.0 (flood) 95.3 505.0 409.7 (flood)

3 (Confluence) 12.6 25.2 12.6 (flood) 40.6 193.0 152.4 (flood)

4 (Confluence) 13.6 24.5 10.9 (flood) 37.0 162.0 125.0 (flood)

5 (Up-Ortega) 17.2 11.3 5.9 (ebb) 32.0 50.3 18.3 (flood)
6 (Up-Cedar) 20.3 15.7 4.6 (ebb) 38.5 105.0 66.5 (flood)


Table A.8 highlights the fact that considerable exchange of sediment may occur between
Zones 2 and 3, and in particular sediment from upstream Ortega and Cedar River including Zone 1
may be ultimately exported to the main-stem. To the extent that the transported sediment is
contaminated, by way of this process contaminants can enter the main-stem. Observe that under
extreme river runoff significant erosion is predicted to occur. Thus a total of 6,630-(653+338) =
5,639 tons/d would erode from the bottom within Zone 3. Given the settling velocity of sediment


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(Table A.4) and the current speeds in the main-stem (Table A.3), it can be easily shown that material
debouched from the mouth of the Ortega can travel -5 km northward during ebb tidal flow and ~3
km southward during flood tidal flow. Since ebb flow in the main-stem is influenced by flow out of
the Ortega (e.g., Figure A.9), the material is likely to be transported along the eastern bank of the
main-stem, toward and possibly beyond Fuller Warren Bridge.






I- Cross-section

6





l3 S




500 0 500 1000 Meters



Figure A.24 Cross-sections at which sediment fluxes are
simulated.

A.4 Concluding Comments
Results of the modeling work point to the need for collection of data on flows and
contaminated sediment sources/distribution/transport in Zone 3. Since available data are neither fully
synchronous nor synoptic, extending the present modeling effort to develop predictive scenarios with
regard to sediment fate in Zone 3 is presently not feasible. Given this constraint, the following data
collection effort is suggested.


A.4.1 Flow Field
The flow field within Zone 3 must be characterized on a one-year basis to include seasonal
effects, by measuring: 1) water levels, 2) wave action and 3) discharges at selected locations to


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enable Eulerian modeling of flow (and hence contaminated sediment motion) within Zone 3. The
location of a wave station (bottom pressure gage) at the mouth of the Ortega River is shown in
Figure A.25. The gage will also record tide (astronomical and storm surge) there. The locations of
two additional tide stations (one in Ortega River and another in Cedar River) are also shown in the
same figure. Velocities and discharges must be obtained at the boundaries of Zone 3 as well as
within the bounded domain. Accordingly, 9 flow cross-sections are selected as shown in Figure
A.26. We recommend the use of the Acoustic Doppler Current Profiler (ADCP) for rapid and
accurate measurement of flow speed. By rapidly traversing each cross-section in a vessel mounted
with an ADCP, the corresponding flow discharge at the cross-section can also be measured. We
recommend that each cross-section be traversed four times at the minimum as follows: 1) "pre-
storm" condition, once during an ebb flow and once during a flood flow, and 2) "during storm"
condition, also once during an ebb flow and once during a flood flow.


Table A.8 Sediment import/export relative to Zone 3
Condition Sediment import/export relative to Zone 3

Ortega River Cedar River Main-stem
(tons/d) (tons/d) (tons/d)

Normal 5.6 (import from) 4.1 (import from) 5.4 (export to)

Extreme river 653 (import from) 338 (import from) 6,630 (export to)
runoff

Wave action 5.9 (import from) 4.6 (import from) 46.4 (import from)
in main-stem

Waves+surge 18.3 (export to) 66.5 (export to) 376 (import from)
in main-stem


A.4.2 Bottom Sediment
For assessing the physical and biogeophysico-chemical nature of bottom sediment within
Zone 3 and its relation to bottom sediment in Zone 2, we recommend an initial plan of bottom coring
at 20 locations shown in Figure A.25. Depending on the findings, coring may need to be extended
further into Zone 2, both in the main-stem and in Ortega and Cedar Rivers upstream of Zone 3. As
noted in Section 4.3.1.3, consideration should be given to the use and efficacy of bottom sediment


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traps as a means to assess sediment transport, especially if high density, near-bottom suspension
layers and considered to be ubiquitous, or even episodically significant, within the study area.


A.4.3 Suspended Sediment

We recommend that suspended sediment data be collected at the same 9 sections as those
shown in Figure A.26 using an ADCP and a dedicated software such as one comprising the Sediview
Method developed by DRL Software Ltd (Dredging Research Ltd., 1999). These "instantaneous"
measurements will also yield the corresponding sediment fluxes across the 9 cross-sections, which
would be critically required for modeling contaminated sediment transport. In addition, we
recommend collection of weekly samples for TSS and particle composition determination at three
sites shown in Figure A.25. Two of these sites should coincide with the sites for tide gages in
upstream Ortega and Cedar Rivers, and the third site with the location of the wave (pressure) gage
at the mouth of the Ortega River.






Coring site
) Pressure gage 0A
Tide gage
.A Water quality











500 0 500 1000 Meters



Figure A.25 Tentative measurement locations for water
level (tide gage), waves (pressure gage), water quality and
bottom coring.


A-26

























500 0 500 1000 Meters


Figure A.26 Cross-sections for current and
turbidity measurements by ADCP.



The use of the ADCP for suspended sediment measurement has been documented (e.g., Land
et al., 1997; Netzband et al., 1999). The method comprising Sediview is conceptually similar to the
(non-commercial) procedure developed by the U. S. Army Corps of Engineers (Fagerburg and Pratt,
1995; Teeter et al., 1996).
With regard to the use of ADCP in the shallow water environment, certain limitations must
be recognized. The main disadvantage is the at information within the bottom -6% of the water
column is not retrieved. In the Zone 3 areas where measurements are to be made, this amounts to loss
of signal from the bottom -30 cm. Thus, in order to "extrapolate" the velocity and suspended
sediment information within this near-bottom zone, it will be essential to make velocity and TSS
measurements on a selective basis using in situ current and turbidity sensors.


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