FINAL 7/8/08 

FLORIDA DEPARTMENT OF ENVIRONMENTAL PROTECTION 

Division of Water Resource Management, Bureau of Watershed Management 

NORTHEAST DISTRICT • LOWER ST. JOHNS BASIN 

TMDL Report 

Total Maximum Daily Load for Nutrients 

for the Lower St. Johns River 

Dr. Wayne Magley and Daryll Joyner 

Watershed Assessment Section 

Bureau of Watershed Management 

Florida Department of Environmental Protection 

2600 Blair Stone Road, MS 3555 

Tallahassee, FL 32399-2400 

June 2008 

 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Table of Contents 

ACKNOWLEDGMENTS ................................................................................................ IV

1. INTRODUCTION ........................................................................................................ 1

1.1 Purpose of Report ............................................................................................ 1

1.2 Development of the TMDL ............................................................................... 1

1.3 Revision of the TMDL ....................................................................................... 1

1.4 Identification of Waterbody ............................................................................. 2

2. STATEMENT OF WATER QUALITY PROBLEM ...................................................... 6

2.1 Verified Nutrient Impairment of the LSJR ...................................................... 6

2.2 Other Indications of Nutrient Impairment....................................................... 7

3. DESCRIPTION OF APPLICABLE WATER QUALITY STANDARDS AND 

WATER QUALITY TARGETS ................................................................................. 9

3.1 Classification of the LSJR and Criteria Applicable to the TMDL .................. 9

3.2 DO Criterion ...................................................................................................... 9

3.3 Nutrient Criterion ............................................................................................ 10

4. DETERMINATION OF CURRENT LOADING ......................................................... 12

4.1 Types of Sources ........................................................................................... 12

4.2 Background .................................................................................................... 12

4.3 Permitted Point Sources ................................................................................ 14

4.3.1 Inventory of Point Sources ................................................................. 14

4.3.2 Estimating Point Source Loads .......................................................... 16

4.3.3 Municipal Separate Storm Sewer System Permittees ...................... 16

4.4 Nonpoint Sources .......................................................................................... 17

4.4.1 Pollution Load Screening Model ........................................................ 17

4.4.2 Atmospheric Deposition ..................................................................... 18

4.4.3 Sediment Flux ...................................................................................... 19

4.5 Loading Inventory .......................................................................................... 19

5. DETERMINATION OF ASSIMILATIVE CAPACITY ................................................ 21

5.1 Use of Modeling .............................................................................................. 21

5.2 Models Used ................................................................................................... 21

5.3 Model Setup .................................................................................................... 24

5.4 Model Calibration ........................................................................................... 24

5.5 Model Results Used To Determine Assimilative Capacity .......................... 25

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

6. DETERMINATION OF THE TMDL .......................................................................... 29

6.1 Expression and Allocation of the TMDL ....................................................... 29

6.2 Load Allocations ............................................................................................ 31

6.3 Wasteload Allocations ................................................................................... 31

6.4 Aggregate Loads and Pollutant Trading ...................................................... 31

6.5 Margin of Safety ............................................................................................. 32

6.6 Seasonal Variability ....................................................................................... 33

7. NEXT STEPS: IMPLEMENTATION PLAN DEVELOPMENT AND BEYOND ........ 34

7.1 Basin Management Action Plan .................................................................... 34

REFERENCES .............................................................................................................. 36

List of Figures 

Figure 1. The Lower St. Johns River .................................................................... 3

Figure 2. Ecological Zones of the Lower St. Johns River Basin ....................... 4

Figure 3. Waterbody Identification Numbers for the Main Stem of the 

LSJR ....................................................................................................... 5

Figure 4. Data Collection and Monitoring Stations of the External Load 

Assessment.......................................................................................... 13

Figure 5. TN Loading to the LSJR by Source Category ................................... 20

Figure 6. TP Loading to the LSJR by Source Category.................................... 20

Figure 7. Model Cells for the LSJR Modeling .................................................... 22

Figure F1. Accuracy of Model DO Predictions for Acosta Bridge ..................... 56

Figure F2. Accuracy of Model DO Predictions for Dames Point ........................ 57

Figure G1. Comparisons of Model Predictions Versus Measured Values for 

Chlorophyll a at Racy Point ................................................................ 59

Figure G2. Comparisons of Model Predictions Versus Measured Values for 

Chlorophyll a at Watson Island .......................................................... 59

Figure G3. Accuracy of Model Predictions of Average Annual Chlorophyll a

for the Freshwater Section.................................................................. 60

Figure G4. Accuracy of Model Predictions for Chlorophyll a Percent 

Exceedances for the Freshwater Section .......................................... 60

List of Tables 

Table 1. Verified Impaired Segments of the Main Stem of the LSJR ............... 7

Table 2. Permitted Wastewater Facilities Discharging to the LSJR............... 15

Table 3. Modeled Variables Included in the CE-QUAL-ICM Model ................. 23

Table 4. Starting Point TN and TP Loads for Point Sources .......................... 27

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Table 5. TMDL Components for the Freshwater Portion of the LSJR ........... 30

Table 6. TMDL Components for the Estuarine Portion of the LSJR .............. 30

Table D1. Summary of Loads to the Lower St. Johns River, 1995. All values in 

metric tons per year. ........................................................................... 49

Table D2. Summary of Loads to the Lower St. Johns River, 1996. All values in 

metric tons per year. ........................................................................... 50

Table D3. Summary of Loads to the Lower St. Johns River, 1997. All values in 

metric tons per year. ........................................................................... 51

Table D4. Summary of Loads to the Lower St. Johns River, 1998. All values in 

metric tons per year. ........................................................................... 52

Table D5. Summary of Loads to the Lower St. Johns River, 1999. All values in 

metric tons per year. ........................................................................... 53

List of Appendices 

Appendix A: The LSJR TMDL Executive Committee............................................... 38

Appendix B: Eutrophication Defined ........................................................................ 39

Appendix C: Basis for LSJR Water Quality Targets ................................................ 40

Appendix D: Estimated Loads to the LSJR, 1995–99 .............................................. 48

Appendix E: Description of State and Federal Stormwater Programs .................. 54

Appendix F: Examples of DO Calibration Figures for the Water Quality Model ... 55

Appendix G: Examples of Chlorophyll a Calibration Figures for the Water 

Quality Model ....................................................................................... 58

Appendix H: Responsiveness Summary to Public Comments on Draft TMDL 

of 2003 .................................................................................................. 61

Appendix I: Annual Average Chlorophyll a Values and TSIs for the LSJR Main 

Stem ...................................................................................................... 75

Appendix J: Allocation Spreadsheets for the Freshwater and Estuarine 

Portions of the LSJR ........................................................................... 76

Appendix K: Ongoing and Proposed Studies by the SJRWMD Designed To 

Revise the TMDL To Address Submerged Aquatic Vegetation 

and Further Evaluate Nutrient Impacts in the Lower St. Johns ....... 80

Appendix L: Site-Specific Alternative Dissolved Oxygen Criterion 

Documentation..................................................................................... 81

Appendix M: Determination of Nitrogen and Phosphorus Nonpoint Loads for 

Urban Stormwater Jurisdictions ...................................................... 101

Appendix N: Comparisons Between Existing 1999 Simulation and TMDL 

Simulation for Marine WBID DO and Freshwater Chlorophyll ....... 124

Appendix O: Responsiveness Summary to Public Comments on Draft TMDL 

following March 2008 Public Meeting .............................................. 129

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

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Florida Department of Environmental Protection 

ACKNOWLEDGMENTS 

The development of this Total Maximum Daily Load (TMDL) was a cooperative effort between 

the Florida Department of Environmental Protection (Department) and the St. Johns River 

Water Management District (SJRWMD). Throughout the several years that this project 

spanned, there was excellent cooperation and coordination between the staff of the two 

agencies, and the Department wishes to express its appreciation to the SJRWMD for its 

cooperative spirit. 

While this was a joint effort between the two agencies, the authors want to acknowledge that the 

main work that constitutes the scientific basis for the Total Maximum Daily Load (TMDL) (the 

determination of the river’s assimilative capacity) was conducted by SJRWMD staff. In 

particular, John Hendrickson and Pete Sucsy should be commended for their outstanding 

contributions and unwavering dedication to completing the modeling work. Thanks to their 

efforts, the water quality model for the Lower St. Johns River (LSJR) is undoubtedly one of the 

best in the nation, and will likely result in improved modeling for other TMDLs as other 

practitioners adopt some of the innovations/adaptations that John and Pete incorporated into 

the LSJR model. 

We also wish to thank and acknowledge the contributions of staff from the Department’s 

Northeast District office. Special thanks are due to Jim Maher and Jeremy Richarde for their 

continuous contributions as technical reviewers and liaison with local stakeholders who 

participated in the meetings of the LSJR Technical Advisory Committee, the TMDL 

Stakeholders Committee, and the TMDL Executive Committee. Their work to develop the 

starting points for the point source loads and the allocation spreadsheets was particularly 

invaluable, and we simply could not have completed the project without their outstanding 

contributions. We also thank former Northeast District Directors Ernie Frey and Mario Taylor 

and current District Director Greg Strong for their dedication to the TMDL Program and their 

leadership of the LSJR Executive Committee. 

Additional thanks are due to Tiffany Busby for her work in facilitating coordination between the 

agencies and with the LSJR Technical Advisory Committee, the TMDL Stakeholders 

Committee, and the TMDL Executive Committee. Finally, we wish to express our appreciation 

for all of the many people who gave their time to participate in the Technical Advisory 

Committee meetings, Stakeholder Committee meetings, and Executive Committee meetings. 

We are confident that the resultant TMDL was improved by everyone who participated in this 

process. 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

1. INTRODUCTION 

1.1 Purpose of Report 

This document presents Total Maximum Daily Loads (TMDLs) for total nitrogen (TN) and total 

phosphorus (TP) for the Lower St. Johns River (LSJR). The river was verified as impaired by 

nutrients based on elevated chlorophyll a and Trophic State Index (TSI) levels in the freshwater 

and marine portions of the river, and was included on Florida’s Verified List of impaired waters 

for the Lower St. Johns River Basin (LSJRB) that was adopted by Secretarial Order on 

September 4, 2003. The TMDLs establish the allowable loadings of TN and TP to the 

freshwater and marine portions of the LSJR that would restore the river so that it meets its 

applicable water quality criteria for nutrients and dissolved oxygen (DO). 

1.2 Development of the TMDL 

This TMDL was developed in cooperation with the St. Johns River Water Management District 

(SJRWMD) as part of its development of Pollutant Load Reduction Goals (PLRGs) for the river. 

In recognition of the eutrophication-related impairment of the river, the Florida Department of 

Environmental Protection (Department) and SJRWMD cooperatively developed a draft Plan of 

Study (POS) for the TMDL (Hendrickson and Magley, 2001) before the river was assessed for 

impairment under Rule 62-303, Florida Administrative Code (F.A.C.) (Identification of Impaired 

Surface Waters Rule, or IWR). As indicated in the POS, the SJRWMD (in conjunction with its 

contractor, the U.S. Army Corps of Engineers [USACE]) was the lead agency for modeling 

activities, including the development of a watershed model to estimate nonpoint source loads 

and the development of a linked hydrologic/water quality model to determine the assimilative 

capacity of the river. 

Both agencies also actively coordinated with a variety of local stakeholders throughout the 

TMDL development process, including meetings to discuss the POS and subsequent monthly 

meetings (for over a year) with the TMDL Stakeholders Committee and the TMDL Executive 

Committee. The TMDL Executive Committee is a broad-based stakeholder group that was 

convened by the Department’s Northeast District in July 2002 (see Appendix A for a list of 

members). It has advised the Department on such issues as water quality targets and 

allocation processes. While the Department is clearly charged with implementing the TMDL 

Program, including the adoption of this TMDL by rule, this TMDL reflects the consensus 

recommendations of the TMDL Executive Committee. 

1.3 Revision of the TMDL 

Florida originally adopted a nutrient TMDL for the LSJR on December 3, 2003 (Rule 62-

304.415, F.A.C.), and formally submitted it to the U.S. Environmental Protection Agency (EPA) 

Region 4 on March 15, 2004. While the EPA initially approved the TMDL on April 27, 2004, the 

agency was challenged on the basis that the Class III marine daily average DO criterion would 

not be met at all times under the TMDL. EPA therefore rescinded its April 27, 2004 approval, 

and subsequently established a nutrient TMDL for the Lower St. Johns River that would meet 

the DO criteria on January 23, 2006. 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

At the time EPA disapproved the state’s TMDL, it recognized that (1) the TMDL for the marine 

portion of the river was based on meeting DO levels that were protective of aquatic life use 

support as an indirect way to evaluate the state’s narrative nutrient criterion (i.e., shall not cause 

an imbalance in flora or fauna); (2) the appropriate DO levels were based on an EPA 

methodology for the development of DO criteria; and (3) the state intended to develop a sitespecific alternative criterion (SSAC) based on the EPA methodology. This acknowledgment 

was specifically mentioned in the introduction to the EPA TMDL document, which stated: 

EPA is aware that FDEP is continuing to pursue development of a site specific 

criterion for dissolved oxygen for the River that would be both protective of aquatic 

life and consistent with the previously submitted TMDL. While EPA’s disapproval 

action triggers EPA’s duty to establish a replacement TMDL, EPA recognizes that the 

FDEP TMDL could be considered for approval in the future should the State adopt 

and EPA approve a site specific criterion. 

This revised document presents a reassessment of the TMDL based on an SSAC for DO for the 

marine portion of the Lower St. Johns River that was adopted by the state and approved by 

EPA. 

1.4 Identification of Waterbody 

The LSJR is that portion of the St. Johns River that flows between the mouth of the Ocklawaha 

River, its largest tributary, and the Atlantic Ocean, encompassing a 2,750-square-mile (mi2

) 

drainage area (Figure 1). Within this reach, the St. Johns River is 101 miles long and has a 

water surface area of approximately 115 square miles. Major centers of population within the 

LSJRB include Palatka, a city of 10,700 at the southern entrance to the basin; Green Cove 

Springs, a city of 4,700 at the midpoint; and the Orange Park, Middleburg, and Jacksonville 

metropolitan area, with a population of over 1 million, in the northern portion of the basin (Floyd 

et al., 1997). The LSJR is a sixth-order, darkwater river estuary, and, along its length, it exhibits 

characteristics associated with riverine, lake, and estuarine aquatic environments (Phlips et al.,

2000). Additional information about the river’s hydrology and geology are available in the Basin 

Status Report for the LSJRB (Department, 2002). 

The LSJR is divided into the following three ecological zones based on salinity (Figure 2): (1) a 

predominantly freshwater, tidal, lakelike zone that extends from the city of Palatka north to the 

mouth of Black Creek; (2) an alternately freshwater and marine, oligohaline zone extending from 

Black Creek northward to the Fuller Warren Bridge (I-95) in Jacksonville; and (3) a 

predominantly marine and much narrower zone downstream from I-95 to the mouth 

(Hendrickson and Konwinski, 1998). 

For assessment purposes, the Department has divided the LSJRB into water assessment 

polygons with a unique waterbody identification (WBID) number for each watershed or stream 

reach. The main stem of the LSJR is divided into 15 segments, as shown in Figure 3. 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure 1. The Lower St. Johns River 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure 2. Ecological Zones of the Lower St. Johns River Basin 

(Note: This figure inadvertently includes Lake George, which is not part of the LSJRB.)

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure 3. Waterbody Identification Numbers for the Main Stem of the LSJR 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

2. STATEMENT OF WATER QUALITY PROBLEM 

2.1 Verified Nutrient Impairment of the LSJR 

Under Section 303(d) of the federal Clean Water Act, states are required to submit to the EPA 

lists of waters that are not fully meeting their applicable water quality standards (designated 

uses). The Department has developed such lists, commonly referred to as 303(d) lists, since 

1992. However, the 1999 Florida Watershed Restoration Act (FWRA) (Section 403.067, Florida 

Statutes [F.S.]) stated that all previous Florida 303(d) lists were for planning purposes only and 

directed the Department to develop, and adopt by rule, a new science-based methodology to 

identify impaired waters. After a long rule-making process, the Environmental Regulation 

Commission (ERC) adopted the new methodology as Rule 62-303, F.A.C. (Identification of 

Impaired Surface Waters Rule, or IWR), in April 2001. The ERC subsequently revised the rule 

in 2006 and 2007. 

The Department used the IWR to assess water quality impairments in the main stem of the 

LSJR in 2003 and verified that the majority of the freshwater and estuarine segments of the river 

are impaired by nutrients (see Table 1). As noted in Table 1, 11 of the 15 LSJR segments were 

verified as impaired by nutrients based on annual mean chlorophyll a concentrations or annual 

mean TSI values. Appendix I provides annual mean chlorophyll a and TSI values for the 

verification period for each segment. 

As required by the FWRA, the Verified List of impaired waters for the LSJR was adopted by 

Secretarial Order (on September 4, 2003) before the original TMDL was adopted by rule. The 

TMDL was subsequently adopted by rule on September 30, 2003, and went into effect on 

December 3, 2003. Impairment associated with parameters other than nutrients will be 

addressed in separate TMDL development efforts in the time frames indicated in the table. 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Table 1. Verified Impaired Segments of the Main Stem of the LSJR 

WBID Waterbody Segment Parameters of Concern Priority for TMDL 

Development

Projected Year 

for TMDL 

Development

2213A STJ RIV AB MOUTH Nutrients (Histchla) Low 2008 

2213A STJ RIV AB MOUTH Iron Medium 2008 

2213B STJ RIV AB ICWW Nutrients (Histchla) Medium 2008 

2213B STJ RIV AB ICWW Lead Medium 2008 

2213B STJ RIV AB ICWW Copper Medium 2008 

2213B STJ RIV AB ICWW Iron Medium 2008 

2213B STJ RIV AB ICWW Nickel Medium 2008 

2213C STJ RIV AB DAMES PT Nutrients (Histchla) (High) (2002) 

2213C STJ RIV AB DAMES PT Copper Medium 2008 

2213C STJ RIV AB DAMES PT Iron Medium 2008 

2213C STJ RIV AB DAMES PT Nickel Medium 2008 

2213D STJ RIV AB TROUT RIV Copper Medium 2008 

2213D STJ RIV AB TROUT RIV Iron Medium 2008 

2213D STJ RIV AB TROUT RIV Nickel Medium 2008 

2213E STJ RIV AB WARREN BRG Nutrients (Chla) (High) (2002) 

2213E STJ RIV AB WARREN BRG Copper Medium 2008 

2213E STJ RIV AB WARREN BRG Iron Medium 2008 

2213F STJ RIV AB PINEY PT Nutrients (Chla) (High) (2002) 

2213I STJ RIV AB BLACK CK Nutrients (TSI) Medium 2008 

2213J STJ RIV AB PALMO CK Nutrients (TSI) Medium 2008 

2213K STJ RIV AB TOCIO Nutrients (TSI) High 2002 

2213L STJ RIV AB FEDERAL PT Nutrients (TSI) High 2002 

2213M STJ RIV AB RICE CK Nutrients (Chla) Medium 2008 

2213N STJ RIV AB DUNNS CK Nutrients (Chla) Medium 2008 

2213G STJ RIV AB DOCTOR LAKE Cadmium Medium 2008 

2213I STJ RIV AB BLACK CK Silver Medium 2008 

Note: Table 1 also includes segments impaired by parameters other than nutrients (certain metals). These parameters are shown 

to provide a complete picture of the impairment in the river, but this TMDL only addresses the nutrient impairment. 

2.2 Other Indications of Nutrient Impairment 

In addition to the elevated chlorophyll a values (algal blooms) and low DO levels, a number of 

widespread water quality problems have been identified throughout the river that are indicative 

of an imbalance in the flora and fauna of the LSJR (Department, 2002). These problems 

include the following: (1) fish kills; (2) submersed aquatic shoreline vegetation covered in algal 

mats; (3) excessive epiphyte growth further blocking light from submerged aquatic vegetation; 

(4) anecdotal accounts of shoreline vegetation losses and reduced recreational fishing quality; 

(5) river sediment conditions indicative of low benthic animal diversity; (6) excessive organic 

matter sedimentation and prolonged anoxia; and (7) the presence of potentially toxic 

dinoflagellates such as the Pfiesteria-like Crytoperidiniopsoids (Burkholder and Glasgow, 

1997a; 1997b) and Prorocentrum minimum (Phlips et al., 2000), often co-occurring with fish kills 

or ulcerative disease syndrome in fish. All of these problems are connected by a common 

thread—they indicate accelerated eutrophication in an estuarine environment (see Appendix B

for a discussion of eutrophication). 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Numerous other studies have identified either high nutrient concentrations or eutrophic 

conditions (Bricker et al., 1999; EPA, 2001; Janicki and Morrison, 2000) in the LSJR. In their 

assessment of nutrient loads to the LSJR and the potential effects, Hendrickson and Konwinski 

(1998) determined the following: 

1. A combination of point and nonpoint source pollution has increased the withinbasin nutrient load to the LSJR 2.4 times over natural background for TN and 6 

times for TP. 

2. Areal nutrient loading, at 9.7 and 2.1 kilograms of nitrogen and phosphorus per 

hectare of watershed contributing area per year in the LSJRB, is one of the 

highest reported from studies in the southeastern United States. 

3. Point sources were the greatest contributor of anthropogenic nutrient load from 

within the basin. However, because this load enters the river nearer to the 

mouth, its incremental effect is presumed to be less than that caused by 

nonpoint sources and upper and middle St. Johns River loads that enter 

upstream. 

4. Changes in the amounts of river algae appear to correlate significantly with 

changes in inorganic nitrogen and DO, suggesting that algae use much of the 

nitrogen supplied to them for growth. During this cycle of growth and ultimate 

death, the algae exert a dominant influence over river oxygen content. 

Based on these findings, it is clear that the LSJR receives high nutrient loads and is nutrient 

enriched, and that it exhibits the symptoms of estuarine eutrophication. While nutrient 

enrichment is not the only problem leading to impaired water quality in the LSJR, it is probably 

the most widespread and multifaceted. 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

3. DESCRIPTION OF APPLICABLE WATER QUALITY 

STANDARDS AND WATER QUALITY TARGETS 

3.1 Classification of the LSJR and Criteria Applicable to the 

TMDL 

The LSJR is a Class III waterbody, with a designated use of recreation, propagation, and the 

maintenance of a healthy, well-balanced population of fish and wildlife. The Class III water 

quality criteria applicable to the impairment addressed by this TMDL are the DO criterion and 

the narrative nutrient criterion. It should be noted that none of the LSJR WBIDs was verified for 

DO impairment using the IWR methodology, which uses a 10 percent exceedance frequency to 

verify impairment. However, continuous DO monitoring data collected in both the freshwater 

and marine reaches of the river (at the Dames Point Bridge station and, to a lesser extent, the 

Acosta Bridge station) from 1996 through 2001 indicated periods when DO concentrations were 

below the criterion in each of these portions of the river. As these values were at levels that 

could adversely impact aquatic fauna, the nutrient TMDL also needed to address the impact of 

nutrients on DO levels. 

 

3.2 DO Criterion 

The applicable Class III DO criterion varies depending on whether a waterbody is 

“predominantly marine”1

 or “predominantly fresh.” The freshwater criterion applies in the 

predominantly freshwater, tidal lakelike zone that extends from the city of Palatka north to the 

mouth of Julington Creek, and in the alternately freshwater and marine, oligohaline zone 

extending from Julington Creek northward to the Fuller Warren Bridge (I-95) in Jacksonville. 

The marine criterion applies in the predominantly marine zone downstream from the Fuller 

Warren Bridge to the mouth. 

The Class III DO criterion for predominantly fresh waters is a minimum DO of 5 mg/L, and the 

criterion for predominantly marine zones is a minimum DO of 4 mg/L, with a minimum daily 

average of 5 mg/L. However, DO levels are known to fluctuate naturally below the DO criterion 

for both predominantly fresh and marine waters in the LSJR, and Florida Water Quality 

Standards (Rule 62-302, F.A.C.) state that natural conditions should not be abated. In Section 

403.021(11), F.S., 2

 the Florida Legislature recognized that water quality can naturally vary 

below the applicable criteria and directed that water quality standards should be reasonably 

established and applied to take natural variability into account. 

 

1 Surface waters in which the surface chloride concentration at the surface is greater than or equal to 1,500 

milligrams per liter (mg/L) are considered “predominantly marine” (Rule 62-302, F.A.C.). 

2 (11) It is the intent of the Legislature that water quality standards be reasonably established and applied to take into 

account the variability occurring in nature. The Department shall recognize the statistical variability inherent in 

sampling and testing procedures that are used to express water quality standards. The Department shall also 

recognize that some deviations from water quality standards occur as the result of natural background conditions. 

The Department shall not consider deviations from water quality standards to be violations when the discharger 

can demonstrate that the deviations would occur in the absence of any human-induced discharges or alterations to 

the waterbody. 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

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Florida Department of Environmental Protection 

To address this natural variation below the criterion, the Department, in cooperation with the 

SJRWMD, evaluated a more appropriate DO target for the estuarine portions of the river using a 

methodology developed by EPA and documented in Ambient Water Quality Criteria for 

Dissolved Oxygen (Salt Water): Cape Cod to Cape Hatteras (EPA, 1999). This methodology 

provides for a more appropriate DO criterion because it addresses both absolute minimum DO 

values for protection against acute effects, and sublethal DO values for protection against 

reductions in growth and recruitment. Under the EPA methodology, these values are combined 

into one relationship, termed the “persistent exposure criteria,” that can be used to evaluate the 

intensity and duration of a given low-DO event. 

The Department’s application of the EPA methodology to develop a SSAC for DO for the marine 

portion of the river between Julington Creek and the mouth was documented in the publication, 

Site Specific Alternative Dissolved Oxygen Criterion to Protect Aquatic Life in the Marine 

Portions of the Lower St. Johns River Technical Support Document (Appendix L). The SSAC 

was expressed as follows: 

The first part of the proposed SSAC is a minimum DO concentration of 4.0 mg/L. In addition, 

the Total Fractional Exposure to DO levels in the 4.0 to 5.0 mg/L range must also be at or below 

1.0 for each annual evaluation period as determined by the equation: 

Max day 55

mg/L 5.0 - 4.8

between Days

Max day 47

mg/L 4.8 - 4.6

between Days

Max day 30

mg/L 4.6 - 4.4

between Days

Max day 21

mg/L 4.4 - 4.2

between Days

Max day 16

mg/L 4.2 - 4.0

between Days

Exposure

Fractional Total <

+

<

+

<

+

<

+

< ⎟ =

⎠

⎞ ⎜

⎝

⎛

Where: 

The number of days within each interval is based on the daily average DO concentration. 

The SSAC was submitted to the ERC in accordance with Subsection 62-302.800(2), F.A.C., and 

was approved by the ERC on May 25, 2006. The Department subsequently submitted it to the 

EPA, and it was subsequently approved by the EPA on October 10, 2006. 

Since this TMDL proposes nutrient reductions to address nutrient impairment, it will only have 

beneficial impacts on DO. Therefore, the TMDL has been evaluated to ensure that nutrient 

reductions in the marine portions of the Lower St. Johns are sufficient to meet the DO SSAC. 

3.3 Nutrient Criterion 

Florida’s nutrient criterion is narrative only—nutrient concentrations of a body of water shall not 

be altered so as to cause an imbalance in natural populations of aquatic flora or fauna. 

Accordingly, a nutrient-related target was needed to represent levels at which an imbalance in 

flora or fauna is expected to occur. While the IWR provides a threshold for nutrient impairment 

for streams and estuaries based on annual average chlorophyll a levels, these thresholds are 

not standards and need not be used as the nutrient-related water quality target for TMDLs. In 

fact, in recognition that the IWR thresholds were developed using statewide average conditions, 

the IWR (Section 62-303.450, F.A.C.) specifically allows the use of alternative, site-specific 

thresholds that more accurately reflect conditions beyond which an imbalance in flora or fauna 

occurs in the waterbody. 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

As part of PLRG development, the SJRWMD established a site-specific threshold for nutrient 

impairment for the freshwater zone based on chlorophyll a values (Hendrickson et al., 2003). 

Hendrickson evaluated the maximum algal biomass levels that would (1) maintain the diversity 

of the plankton community, (2) facilitate the upward transfer of primary production to higher 

trophic levels (and maintain zooplankton diversity), and (3) minimize the potential dominance of 

detrimental algal species and the production of algal toxins. He found that a chlorophyll a target 

of 40 micrograms per liter (μg/L), not to be exceeded more than 10 percent of the time, would 

protect the aquatic flora and fauna of the river. Studies have shown that when chlorophyll a

levels rise above 40 μg/L, a shift in algal types occurs: blue-green algae begin to dominate the 

system, toxic algal species begin to increase, and zooplankton communities begin to decline. 

This alternative threshold for the freshwater portion of the river was discussed extensively at 

several meetings of the LSJR TMDL Stakeholders Committee and TMDL Executive Committee, 

and both groups recommended it be used for this TMDL rather than the IWR threshold. These 

groups also recommended that the threshold be applied over a long-term period (several years 

representing slightly drier than average conditions), rather than a worst-case, dry year. The 

Department agreed with these recommendations and established the TMDL using the 

alternative chlorophyll a threshold and long-term average model output, rather than model 

predictions for a worst-case year. 

Maintaining chlorophyll a levels below 40 μg/L 90 percent of the time should prevent an 

imbalance in natural populations of aquatic flora and fauna under average conditions, and 

combined with other conservative aspects of the modeling (focusing on the worst-case WBID, 

for example) should protect the river during low-flow conditions as well. However, there is some 

uncertainty whether these levels will be fully protective in this portion of the river under critical, 

low-flow conditions or during the extended growing season with less than average flows. For 

this reason, the river system will continue to be evaluated to determine if a seasonal average 

maximum or yearly average maximum level of chlorophyll a should be established to protect 

against imbalances in natural populations of aquatic flora and fauna. 

Specifically, studies will be conducted to demonstrate the following: (1) that progress is being 

made towards reducing nutrient loads by the amount required under the TMDL (30 percent) or 

that progress towards reaching the percent reduction goal is being made; (2) that once the 30 

percent reduction goal is reached, it results in chlorophyll a levels that do not exceed 

40 μg/L more than 10 percent of the time; and (3) that once the chlorophyll a target is reached, 

it has resulted in the achievement of the narrative nutrient criterion (i.e., balanced, natural 

populations of aquatic flora and fauna). 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

4. DETERMINATION OF CURRENT LOADING

4.1 Types of Sources 

An important part of the TMDL analysis is the identification of source categories, source 

subcategories, or individual sources of nutrients in the watershed and the amount of pollutant 

loading contributed by each of these sources. Sources are broadly classified as either “point 

sources” or “nonpoint sources.” Historically, the term “point sources” has meant discharges to 

surface waters that typically have a continuous flow via a discernable, confined, and discrete 

conveyance, such as a pipe. Domestic and industrial wastewater treatment facilities (WWTFs) 

are examples of traditional point sources. In contrast, the term “nonpoint sources” was used to 

describe intermittent, rainfall-driven, diffuse sources of pollution associated with everyday 

human activities, including runoff from urban land uses, runoff from agriculture, runoff from 

silviculture, runoff from mining, discharges from failing septic systems, and atmospheric 

deposition. 

However, the 1987 amendments to the Clean Water Act redefined certain nonpoint sources of 

pollution as point sources subject to regulation under the EPA’s National Pollutant Discharge 

Elimination System (NPDES) Program. These nonpoint sources included certain urban 

stormwater discharges, including those from local government master drainage systems, 

construction sites over five acres, and a wide variety of industries (see Appendix E for 

background information on the state and federal stormwater programs). 

To be consistent with Clean Water Act definitions, the term “point source” will be used to 

describe traditional point sources (such as domestic and industrial wastewater discharges) AND

stormwater systems requiring an NPDES stormwater permit when allocating pollutant load 

reductions required by a TMDL (see Section 6). However, the methodologies used to estimate 

nonpoint source loads do not distinguish between NPDES stormwater discharges and nonNPDES stormwater discharges, and as such, this source assessment section does not make 

any distinction between the two types of stormwater. 

4.2 Background 

This section describes the approach used to determine external nutrient loads to the LSJR. The 

external load assessment was intended to determine (1) the spatial and temporal characteristics 

of the external load to the LSJR and, ultimately, (2) the effectiveness and costs associated with 

strategies for reducing this load. Assessing the external load entailed monitoring and research 

projects to determine the volume, concentration, timing, location, and underlying nature of point, 

nonpoint, and atmospheric source additions to the river stem and tributary mouths below the 

head of tide. The subsections below describe the approaches used for assessing each of these 

major external load categories. Figure 4 identifies tributary water quality sampling stations, 

stream gauging stations, and major point sources in the basin. Because the computations 

involved in the development of the external load for the LSJR are so instrumental in the 

outcome of TMDLs and PLRGs, they were reported in a separate document (Hendrickson et al.,

2003). 

 12 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure 4. Data Collection and Monitoring Stations of the External Load Assessment 

 13 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

4.3 Permitted Point Sources 

4.3.1 Inventory of Point Sources 

There are 36 permitted wastewater treatment facilities that discharge nutrient loads directly into 

the LSJR (Table 2): 32 domestic wastewater facilities and 4 industrial wastewater facilities. 

These facilities, which are permitted through the NPDES Program, are estimated to contribute 

approximately 27 and 55 percent of the annual average above-background TN and TP loads, 

respectively, to the LSJR. 

Domestic wastewater facilities that discharge to surface waters are concentrated along the St. 

Johns River from Green Cove Springs to its mouth north of Jacksonville, and farther south near 

Palatka. The largest domestic wastewater dischargers in the basin are the wastewater 

treatment facilities associated with the city of Jacksonville in the northern (downstream) end of 

the basin, including the Buckman Street, Arlington East, JEA District II, Southwest District, and 

Mandarin wastewater treatment facilities. Several of these facilities participate in reuse 

programs, and most are seeking ways to either include or improve nutrient removal treatment 

(Department, 1997; Hendrickson and Konwinski, 1998). 

All domestic wastewater facilities discharging to the St. Johns River are required, at a minimum, 

to monitor for conventional pollutants such as total suspended solids (TSS), carbonaceous 

biological oxygen demand (CBOD5), and fecal coliform bacteria (Department, 1997). While 

most permits do not include nutrient effluent limits, nutrients must be monitored in many 

systems because of their potential negative effects on surface water, including their role in the 

formation of nuisance and harmful algal blooms. 

Large industrial dischargers in the basin include power plants, pulp and paper mills, chemical 

plants, and manufacturing plants. The majority of industrial plants send their process 

wastewater through pretreatment facilities to publicly owned treatment works (POTWs) such as 

the Buckman plant. Facilities with significant nutrient discharges to the main stem of the LSJR 

include the Georgia-Pacific Corporation (which produces bleached and unbleached pulp and 

paper), Smurfit-Stone Container (which changed from a pulp and paper mill to a recycling mill in 

the 1990s, reducing the volume of discharge), and Anheuser-Busch (a brewery). Remaining 

discharges include nonprocess wastewater, such as cooling water, softener regenerate, and 

boiler blowdowns, that do not contribute a significant nutrient load. 

The original modeling work did not consider the Seminole Electric Power Plant near Palatka as 

a significant source of nutrients because its discharge is primarily once-through cooling water. 

However, during the permit renewal process, representatives of Seminole Electric indicated that 

there was a net increase in nitrogen loads to the St. Johns from the discharge, and a nitrogen 

load of 5,724 kilograms per year (kg/yr) from this facility was added to WBID 2213L (there is no 

net increase in phosphorus loads for the facility). 

 14 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Table 2. Permitted Wastewater Facilities Discharging to the LSJR 

Name of Facility Facility ID 

Permitted 

Flow 

(mgd) 

1997–98 Nutrients 

TN 

(mg/L) 

TP 

(mg/L) 

Smurfit-Stone Container Corporation FL0000400 20 6.8 1.1 

Jefferson Smurfit – JAX FL0000892 6 8.8 1.2 

USN – NS Mayport WWTF FL0000922 2 3.2 2.1 

USN – NAS Jacksonville WWTF FL0000957 3 8.5 1.7 

Georgia-Pacific FL0002763 40 5.5 1.4 

Jacksonville Beach WWTF FL0020231 4.5 9.1 2.2 

Neptune Beach WWTF FL0020427 1.5 8.8 1.4 

Green Cove Springs – Harbor Road WWTF FL0020915 0.75 9.2 2.9 

Westminster Woods – (Wesley Manor 

Retirement Village) FL0022489 0.09 4.6 2.0 

Atlantic Beach – Buccaneer WWTF FL0023248 1.9 13.4 1.4 

JEA – Mandarin WWTF FL0023493 7.5 5.34 2.3 

JEA – Monterey WWTF (operated by UWF) FL0023604 3.6 11.3 2.6 

JEA – Holly Oaks WWTF (formerly UWF) FL0023621 1 8.3 2.1 

JEA – San Jose WWTF (formerly UWF) FL0023663 2.25 10.0 2.9 

JEA – Jacksonville Heights WWTF (formerly 

UWF) FL0023671 2.5 10.1 2.9 

Orange Park WWTF FL0023922 2.5 - 3.7 

JEA – San Pablo WWTF (formerly UWF) FL0024767 0.75 6.5 3.5 

CCUA – Miller Street WWTF FL0025151 4.99 4.5 3.2 

JEA – Ortega Hills WWTF (formerly UWF) FL0025828 0.22 16.8 2.3 

JEA – Buckman WWTF FL0026000 52.5 10.5 4.7 

JEA – Arlington WWTF FL0026441 20 14.3 2.6 

JEA – Northeast WWTF (aka JEA – District II 

WWTF) FL0026450 10 22.7 5.9 

JEA – Southwest WWTF FL0026468 10 10.5 1.4 

JEA – Royal Lakes WWTF (formerly UWF) FL0026751 3.25 7.8 3.8 

FWSC – Beacon Hills SD WWTF FL0026778 1.3 11.9 2.0 

FWSC – Woodmere SD WWTF FL0026786 0.7 11.6 1.7 

Green Cove Springs – South WWTF FL0030210 0.5 13.6 2.3 

CCUA – Fleming Oaks WWTF FL0032875 0.49 3.0 1.9 

Atlantic Beach – Main WWTF (D001) FL0038776 3 11.4 2.1 

Palatka WWTF FL0040061 3 14.7 2.4 

Anheuser Busch – Main St. – Land Application FL0041530 2.6 3.9 0.3 

Hastings WWTF FL0042315 0.12 4.5 0.6 

JEA – Julington Creek WWTP FL0043591 0.476 12.0 3.0 

CCUA – Fleming Island WWTF (combined) FL0043834 6.365 - - 

UWF – Saint Johns North WWTF FL0117668 - 6.5 1.7 

Brierwood SD – Beauclerc STP FL0023370 - - - 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

4.3.2 Estimating Point Source Loads 

Point source effluent loads were calculated through a combination of monitoring data and 

statistical extrapolation to fill monitoring gaps. Point source loads were estimated for only those 

facilities that discharge directly to the LSJR or to tributary mouths below the head of tide. 

Monthly operating report data from treatment facilities were used to create a time-varying input 

dataset for effluent flow and nutrient, suspended solids, and biological oxygen demand 

concentrations. Weekly, monthly, or quarterly monitoring data for water quality concentrations 

were multiplied by daily flow data to determine the daily load. For facilities that lacked complete 

chemistry data, mean values from the facility or from similar facilities were used to complete the 

missing record. 

Water quality monitoring data collected for facilities during a 1993–95 point source assessment 

project were also available and were combined into a geographic information system (GIS) 

database that also includes outfall locations and sewer service coverage area. Outfall locations 

were then used to identify the appropriate model grids where these sources entered the system. 

4.3.3 Municipal Separate Storm Sewer System Permittees 

Like other nonpoint sources of pollution, urban stormwater discharges are associated with land 

use and human activities, and are driven by rainfall and runoff processes leading to the 

intermittent discharge of pollutants in response to rainstorms. The 1987 amendments to the 

federal Clean Water Act designated certain stormwater discharges from urbanized areas as 

point sources requiring NPDES stormwater permits. The three major components of the 

NPDES stormwater regulations are as follows: 

• Municipal Separate Storm Sewer System (MS4) permits that are issued to entities 

that own and operate master stormwater systems, primarily local governments. 

Permittees are required to implement comprehensive stormwater management 

programs designed to reduce the discharge of pollutants from the MS4 to the 

maximum extent practicable. 

• Stormwater associated with industrial activities, which is regulated primarily by a 

multisector general permit that covers various types of industrial facilities. 

Regulated industrial facilities must obtain NPDES stormwater permit coverage and 

implement appropriate pollution prevention techniques to reduce the 

contamination of stormwater runoff. 

• Construction activity generic permits for projects that ultimately disturb one or 

more acres of land and that require the implementation of stormwater pollution 

prevention plans to provide for erosion and sediment control during construction. 

In addition to the NPDES stormwater construction permitting regulations, Florida was the first 

state in the country to require the treatment of stormwater for all new developments with the 

adoption of the Stormwater Rule in late 1981. The Stormwater Rule is a technology-based 

program that relies on the implementation of best management practices (BMPs) that are 

designed to achieve a specific level of treatment (i.e., performance standards) as set forth in 

Rule 62-40, F.A.C. In 1994, state legislation created the Environmental Resource Permitting 

 16 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Program to consolidate stormwater quantity, stormwater quality, and wetlands protection into a 

single permit. Currently, the majority of Environmental Resource Permits are issued by the 

state’s water management districts, although the Department continues to do the permitting for 

specific projects. 

The NPDES Stormwater Program was implemented in phases, with Phase I MS4 areas 

including municipalities having a population above 100,000. Because the master drainage 

systems of most local governments in Florida are interconnected, the EPA implemented Phase 

1 of the MS4 permitting program on a countywide basis, bringing in all cities, Chapter 298 urban 

water control districts, and the Florida Department of Transportation (FDOT) throughout the 15 

counties meeting the population criteria. Phase II of the NPDES Program was expanded in 

2003 and requires stormwater permits for construction sites between 1 and 5 acres, and for 

local governments with as few as 10,000 people. 

Although MS4 discharges are technically referred to as “point sources” for the purpose of 

regulation, they are still diffuse sources of pollution that cannot be easily collected and treated 

by a central treatment facility. All Phase 1 MS4 permits issued in Florida include a reopener 

clause allowing permit revisions for implementing TMDLs once they are formally adopted by 

rule. Florida’s Phase II MS4 Generic Permit has a “self-implementing” requirement once 

TMDLs are adopted that requires the MS4 permittee to update its stormwater management 

program as needed to meet its TMDL allocations. 

Within the LSJRB, the stormwater systems owned and operated by local governments and 

FDOT within the urbanized areas of Duval County are covered by an NPDES MS4 permit. 

Additionally, several other local governments in the basin have applied for coverage under the 

Phase 2 NPDES MS4 permit. Within Clay, Duval, Flagler, and St. Johns Counties, 223 

industrial facilities have received coverage under the multisector generic permit or the noexposure exemption. 

4.4 Nonpoint Sources 

Nonpoint sources of nutrient loading to the LSJR include septic tanks, marinas, silviculture, row 

crop agriculture, dairies, stormwater from urban development and tributaries (including Black 

Creek, Dunns Creek, Deep Creek, Rice Creek, Julington Creek, Trout Creek, Sixmile Creek, 

Governors Creek, Clarkes Creek, Cedar Creek, Camp Branch, Mill Branch, and Dog Branch). 

Unlike traditional point source effluent loads, nonpoint source loads enter at so many locations 

and exhibit such large temporal variation that a direct monitoring approach is infeasible except 

for the largest, most significant inputs. Those largest inputs are the upstream boundary of the 

LSJR at Buffalo Bluff, Dunns Creek, and the downstream boundary at the Atlantic Ocean. For 

all other nonpoint entry points, watershed modeling was used to complete the external load 

budget. As part of the revised TMDL, additional nonpoint loading from the Pablo Creek 

watershed was incorporated into the model. 

4.4.1 Pollution Load Screening Model 

The watershed model used to estimate nonpoint source loads was the Pollution Load Screening 

Model (PLSM) (Adamus and Bergman, 1995; Hendrickson and Konwinski, 1998). The PLSM 

uses a computer-driven GIS framework to develop aggregate whole-basin loads of relevant 

water quality constituents. The computational approach of the PLSM calculates constituent load 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

as the product of concentration and runoff water volume, using nonpoint source pollutant export 

concentrations specific to 1 of 15 different land use classes, and water quantity through a hybrid 

of the Soil Conservation Service (SCS) curve number method. 

In the LSJR application, four significant modifications were made to the model framework, as 

follows: 

1. The model time step was shortened to seasonal, rather than annual 

average loading rates, to account for seasonal differences in specific land 

use export concentrations and runoff quantity; 

2. Eight additional water quality variables were added: orthophosphate, 

total inorganic nitrogen, labile (easily broken down) organic carbon, 

nitrogen, phosphorus, and refractory (slowly broken down) organic 

carbon, nitrogen, and phosphorus; 

3. Land-use loading rates were adjusted to monitoring data collected in the 

LSJRB using a linear multiple regression best-fit approach based on 

contributing land use fractions in calibration watersheds; and 

4. Hydrologic predictions were improved by using an adjusted water quantity 

based on the deviations in long-term rainfall patterns. 

4.4.2 Atmospheric Deposition 

A review by Paerl (1993) showed that atmospheric deposition contributes 10 to 50 percent to 

the nitrogen budget of estuaries worldwide. In Chesapeake Bay, it is estimated that 25 percent 

of the human-caused nitrogen load originates as atmospheric deposition (Fisher and 

Oppenheimer, 1991). In Tampa Bay, atmospheric deposition provides 29 percent of the total 

nitrogen load (Pribble and Janicki, 1998), making it the second leading source of nitrogen to the 

bay (Greening et al., 1997). 

In their original calculation of nutrient budgets for the LSJR, Hendrickson and Konwinski (1998) 

estimated that atmospheric wet deposition contributed 15 percent of the total inorganic nitrogen 

to the river on an annual average basis and 21 percent during the peak algal bloom season, 

from April through July. However, a reporting unit error was subsequently discovered, and the 

estimated contribution from atmospheric deposition was reduced to about 4 percent per year. 

Due to the coarseness of this original estimate, a more detailed atmospheric deposition load 

assessment was deemed necessary. 

A recently completed assessment of atmospheric deposition load to the LSJR (Pollman and 

Roy, 2003) determined that approximately 2 percent of the total nitrogen load, and 10 percent of 

the inorganic nitrogen load, is supplied through direct atmospheric deposition. The objective of 

this assessment was to increase the precision of the atmospheric load estimate and to 

determine if spatially and temporally varying input is needed to adequately describe nutrient 

enrichment. The assessment also included a greater number of nutrient forms, dry and wet 

deposition, an increased number of stations, and an examination of existing data. 

 18 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Atmospheric deposition of phosphorus was not included in the modeling and TMDL assessment 

because it is expected to be a very minor source of phosphorus to the basin. 

4.4.3 Sediment Flux 

The bottom sediment–water interface represents an important boundary for the exchange of 

nutrients, carbon, and oxygen. As such, the upward and downward flux of these constituents 

must be assessed to properly account for the water quality characteristics of the water column. 

This is particularly true of broad, shallow, slow-moving rivers such as the LSJR, where positive 

(i.e., upward) flux from the sediment undoubtedly makes up a significant portion of the 

bioavailable nutrient load during certain times of the year. While river sediments represent a 

transient source of relevant constituents, sediments differ from other sources in that they are not 

a net positive source (i.e., not a true external source), and hence are not listed as a general 

allocation category in the following section. Over the long term, the accrual of material to the 

sediment is positive, and long-term net upward sediment flux is negative. In general, long-term 

net accrual to the sediments is proportional to the sources to a particular river reach; thus the 

effect exerted by transient upward nutrient flux can likewise be considered proportional to the 

external sources. 

Several studies have been performed to quantify the composition and accretion rate of LSJR 

sediments. Presentations at the October 14–15, 2002, St. Johns River Symposium by Malecki 

and White; Jaeger and Mausner; Chavan and Ogram; and DePinto, Kaur, and Bierman Jr. 

summarized findings from these studies. The studies were designed specifically to provide 

input data necessary for dynamic sediment flux modeling for the LSJR TMDL and PLRG 

determination. 

4.5 Loading Inventory 

Appendix D (Tables D1 through D5) shows estimated nonpoint source loads for the LSJR, and 

Figures 5 and 6 summarize TN and TP loads for 1995 through 1999, respectively. As noted in 

the pie charts, upstream sources are the dominant TN load to the LSJR, while LSJR nonpoint 

and point source TP loads are roughly equivalent to the upstream TP load. 

 19 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure 5. TN Loading to the LSJR by Source Category 

Lower St. Johns River Nitrogen Load Summary

1995–99

 Upstream (Middle St. Johns,

 Ocklawaha, and Crescent Lake

 LSJR Basin Nonpoint Source

 LSJR Basin Point Source

Dotted - Anthropogenic

Clear - Natural Background

Figure 6. TP Loading to the LSJR by Source Category 

Lower St. Johns River Phosphorus Load Summary

1995–99

 Upstream (Middle St. Johns,

 Ocklawaha, and Crescent Lake

 LSJR Basin Nonpoint Source

 LSJR Basin Point Source

Dotted - Anthropogenic

Clear - Natural Background

 20 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

5. DETERMINATION OF ASSIMILATIVE CAPACITY 

5.1 Use of Modeling 

Nutrient enrichment and the resulting problems related to eutrophication are usually widespread 

and are frequently manifested at a distance (in both time and space) from their source. 

Addressing eutrophication involves relating water quality and biological effects (such as 

photosynthesis, decomposition, and nutrient recycling), as acted upon by hydrodynamic factors 

(such as flow, wind, tide, and salinity) to the timing and magnitude of constituent loads supplied 

from various categories of pollution sources. Dynamic computer simulation models have 

become indispensable tools to describe these relationships. Calibrated models also provide 

opportunities to predict water quality conditions under alternative constituent loadings. 

5.2 Models Used 

An interconnected suite of basinwide hydrologic, hydrodynamic, and water quality models was 

assembled to develop this TMDL. The suite of models includes the following: (1) a hydrologic 

model that calculates seasonal runoff and nutrient loads for each sub-basin within the LSJRB 

(PLSM, described previously); (2) a hydrodynamic model of the river that simulates the mixing 

and transport of nutrients in the river; and (3) a water quality model that simulates the 

transformation of nutrients and processes affecting eutrophication in the river. 

The river hydrodynamics and salinity of the LSJR were simulated with the Environmental Fluid 

Dynamics Code (EFDC) model (Hamrick, 1992; Sucsy and Morris, 2002). The EFDC solves 

finite-differenced forms of the hydrostatic Navier-Stokes equations, together with a continuity 

equation, and transport equations for salinity, temperature, turbulent kinetic energy, and 

turbulent macroscale. The equations are solved horizontally on a curvilinear, orthogonal grid 

and vertically on a stretched sigma-grid. Figure 7 illustrates the grid used for both the 

hydrodynamic and water quality models. This grid is composed of 2,210 horizontal cells and 6 

vertical layers. The mean cell length is 492 meters, and the maximum achievable time-step for 

stability of the hydrodynamics simulation is approximately 30 seconds. With the EFDC 

application to the LSJR, remarkably precise simulations of tidal range, tidal occurrence, and 

river flow have been achieved (Sucsy and Morris, 2002). 

The three-dimensional, time-variable water quality process model code used was the USACE 

Quality Integrated Compartment Model (CE-QUAL-ICM), Version 2 (Cerco and Cole, 1993). 

CE-QUAL-ICM is among the most sophisticated water quality process models in existence and 

was originally developed for the Chesapeake Bay Program to examine factors leading to bay 

hypoxia. Version 1 of the model contained 22 variables that simulated oxygen dynamics and 

included the interaction of 3 phytoplankton groups, nutrients, and organic carbon. A benthic 

sediment diagenesis submodel was dynamically coupled with the water column to produce 

sediment oxygen demand and nutrient fluxes. In its current version, the model has been 

expanded to include compartments for benthos, zooplankton, and submerged aquatic 

vegetation. Table 3 summarizes the variables included in the LSJR version of the CE-QUALICM model. 

 21 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure 7. Model Cells for the LSJR Modeling 

 22 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Table 3. Modeled Variables Included in the CE-QUAL-ICM Model 

Model State Variables 

Nitrate + nitrite nitrogen Internal phosphorus, algal group 1 

Ammonium nitrogen Internal phosphorus, algal group 2 

Urea Internal phosphorus, algal group 3 

Refractory dissolved organic nitrogen Refractory dissolved organic carbon 

Labile dissolved organic nitrogen Labile dissolved organic carbon 

Refractory particulate organic nitrogen Refractory particulate organic carbon 

Labile particulate organic nitrogen Labile particulate organic carbon 

Total nonvolatile suspended solids Green algae biomass as carbon 

Dissolved orthophosphate P Cyanobacteria biomass as carbon 

Particulate inorganic P Diatoms biomass as carbon 

Refractory dissolved nonorthophosphate P Temperature 

Labile dissolved nonorthophosphate P Salinity 

Refractory particulate nonorthophosphate P Dissolved oxygen 

Labile particulate nonorthophosphate P Available silica 

Chemical oxygen demand Particulate biogenic silica 

Sediment Model 

State Variables Sediment-Water Flux 

Temperature 

Particulate organic carbon Sediment oxygen demand 

Sulfide/methane Release of chemical oxygen demand 

Particulate organic nitrogen 

Ammonium Ammonium flux 

Nitrate Nitrate flux 

Particulate organic phosphorus 

Phosphate Phosphate flux 

Particulate biogenic silica 

Dissolved silica Silica flux 

Benthic algal biomass Dissolved oxygen, nutrients 

State Variables for Submersed Aquatic Vegetation 

Deposit feeding benthos as carbon Filter feeding benthos as carbon 

Micro zooplankton as carbon Meso zooplankton as carbon 

Submerged aquatic vegetation (SAV) shoot biomass as 

carbon SAV root biomass as carbon 

Epiphyte biomass on SAV as carbon Inorganic suspended solids 

Benthic algae as carbon 

 23 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

The USACE Research and Development Center (ERDC) applied CE-QUAL-ICM to the LSJR 

through a combination of modifications to existing subroutines and through the development of 

new subroutines and state variables, where appropriate. LSJR–EFDC hydrodynamics were 

linked to CE-QUAL-ICM. 

New subroutines were added to the water quality model, including processes for the 

photochemical decomposition of colored dissolved organic matter, nitrogen fixation by one of 

the phytoplankton groups, and a flocculation subroutine to account for the transfer of organic 

carbon from the dissolved to particulate phase at the turbidity maximum. New state variables 

added included refractory dissolved organic carbon, nitrogen, and phosphorus. The full 

sediment diagenesis submodel was utilized and three phytoplankton compartments were 

simulated (freshwater blue-green algae, freshwater diatoms, and marine diatoms). Both Tillman 

et al. (2004) and Sucsy and Hendrickson (2004) document the modifications to CE-QUAL-ICM 

that were made for this application of the model. 

Key changes to the oligohaline/mesohaline component of the water quality model included the 

following: 

 

1. Separation of the algal communities into a freshwater group and a marine group, 

with optimum salinities of 5 parts per thousand (ppt) and 20 ppt, respectively; 

2. A 50 percent increase in the values for KLDC (the labile dissolved organic carbon 

dissolution rate) and KLPC (the labile particulate organic carbon dissolution rate), 

from 0.05/day to 0.075/day; 

3. Revision such that all organic carbon from predation was labile; and 

4. A new subroutine to allow for nitrogen fixation by one of the phytoplankton groups. 

5.3 Model Setup 

Hendrickson and Konwinski (1998) described the setup of the PLSM to provide daily flows and 

loads from contributing sub-basins to the St. Johns River. Figure 7 shows points in the 

hydrodynamic/water quality grid where sub-basin and point source contributions enter. The 

upstream boundary for the EFDC and CE-QUAL-ICM models was placed at Buffalo Bluff where 

total daily river discharge is recorded. Water quality measurements are also routinely collected 

at Buffalo Bluff and were used to define time variable boundary loads. The downstream 

boundary for the EFDC and CE-QUAL-ICM models included a tidal water-level open-ocean 

boundary and a time series of water quality measurements. 

5.4 Model Calibration 

Sucsy and Morris (2002) described the calibration procedure and presented hydrodynamic 

model results for the January 1, 1995 through November 30, 1998 calibration period. The 

calibration of the EFDC involved examination and adjustments to the following data and input 

parameters: bottom bathymetry, bottom roughness, tidal water level at the open-ocean 

boundary, the specification of an adequate number of vertical layers, and the specification of a 

nonreflective upstream open boundary. 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

The model was first calibrated for only the M2 tide, but then the following components were 

added: (1) low-frequency, subtidal water level at the ocean boundary; (2) main stemflow at 

Buffalo Bluff; (3) dynamically-coupled salinity; (4) tributary inflows; and (5) meteorologic 

components for wind, rainfall, and evaporation. Sucsy and Morris (2002) describe error 

analytical techniques used to compare observed and simulated results. These techniques 

include (a) regression analysis, (b) calculation of median relative error, (c) comparison of 

means, (d) calculation of root mean square error (RMSE), and Kologorov-Smirnov tests for 

determining the likelihood that two sample populations have identical cumulative distribution 

functions. 

The calibrated EFDC model was provided to the ERDC for linkage to the modified CE-QUALICM model (June 2000). The ERDC was contracted to provide a model calibrated to data 

collected from the period from December 1, 1995, through November 30, 1998. SJRWMD staff 

performed skill assessments of the model using data collected outside the calibration period 

(1995, 1996, and 1999). Because of the dramatic differences that occurred in the high-flow and 

low-flow years of 1998 and 1999, the calibration effort was shifted to these two years to better 

encompass the total potential environmental variation. 

Sucsy and Hendrickson (2004), and Tillman et al. (2004) present the calibration and verification 

results for the water quality model. Some of the same analytical techniques used to evaluate 

the hydrodynamic calibration were used to evaluate the calibration of key water quality 

parameters at long-term monitoring sites. Appendix F (Figures F1 and F2) shows examples of 

the results from a RMSE analysis of DO predictions at Acosta Bridge and Dames Point, 

respectively, and Appendix G (Figures G1 through G4) shows the calibration results for 

chlorophyll a. 

5.5 Model Results Used To Determine Assimilative Capacity 

Based on a recommendation from the LSJR TMDL Executive Committee, point sources directly 

discharging to the St. Johns were evaluated based on their 1997–98 discharge flows and loads, 

with an allowance for anticipated growth over the next few years (rather than assuming 

permitted design flows and loads). Table 4 summarizes the starting conditions assumed for 

each facility that were considered as part of the TMDL process. Nonpoint source contributions 

to the river varied in response to fluctuations in annual rainfall. 

The LSJR TMDL Executive Committee also recommended the addition of two discharges to the 

TMDL simulations to represent future domestic wastewater discharges under the Apricot Act 

requirements (advanced wastewater treatment and discharge only during wet weather) and 

reverse osmosis (RO) discharges to the St. Johns into the freshwater portion (WBID 2213I) and 

marine portion (WBID 2213H). The annual freshwater discharge load was set at 9,961 kg/yr TN 

and 3,320 kg/yr TP. In the marine portion, an annual discharge load of 4,979 kg/yr TN was 

used. 

Appendix M describes the methodology used to determine projected growth in the basin 

through 2008 and how changes in urban stormwater were associated with various jurisdictions. 

These changes were incorporated into the TMDL simulation and are reflected in the allocation 

spreadsheets found in Appendix J. 

The SJRWMD staff presented results from model simulations for the freshwater zone for 1995, 

1997, 1998, and 1999. Each year was evaluated with respect to whether the predicted 

 25 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

chlorophyll a levels met the alternative chlorophyll a threshold of 40 μg/L less than 10 percent of 

the time. 

Sucsy and Hendrickson (2004) described the process of assessing the relative influence of 

anthropogenic nitrogen and phosphorus loads from point and nonpoint sources and the 

upstream boundary by simulating incremental reductions (25 percent, 50 percent, 75 percent, 

and 100 percent) to the river. The exceedance of the alternative chlorophyll a target was 

calculated for each year, along with the estimated reduction in the anthropogenic load 

necessary to meet the target. Based on the long-term average results for the 4 years, the 

SJRWMD-recommended PLRG was a 30 percent reduction in anthropogenic point, nonpoint, 

and upstream boundary nitrogen and phosphorus loads. 

A similar analysis was completed for the combined oligohaline/mesohaline portion of the river. 

In these zones, model DO predictions were evaluated to determine whether the “persistent 

exposure criterion” impairment index (1.0) was met for each set of incremental reductions for 

each model year (Hendrickson et al., 2003). In this portion of the river, nitrogen was the key 

nutrient that needed to be reduced to meet the target. Due to depressed DO conditions and a 

large fish kill in 1999, 1999 was selected as the period to establish nitrogen load reductions to 

protect the ecological health of the aquatic community. The modeling indicated that a 28.5 

percent reduction in anthropogenic point and nonpoint nitrogen loads was needed from within 

this reach to attain the DO SSAC (percent reductions were calculated based on the initial 

starting points used by the SJRWMD for 1997–98). This load reduction was contingent on the 

30 percent reduction occurring in the upstream, freshwater reach. 

It should be noted that the loading capacities of both portions of the river were originally 

determined by interpolation and that the interpolated loading capacities were then used to 

develop detailed wasteload and load allocations. To confirm that the interpolated values (and 

resultant allocations) would achieve water quality standards, a final model run was made with 

modeled loads set at the allocated loads. Appendix N presents comparisons between 

simulation results for the existing 1999 scenario and the final TMDL scenario for both the marine 

(DO) and freshwater (chlorophyll) portions. 

 26 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Table 4. Starting Point TN and TP Loads for Point Sources 

Name of Facility 

Current 

Flow 

(mgd) 

Projected 

Increase 

(mgd) 

Permitted 

Flow 

(mgd) 

Starting 

Point 

Flow 

(mgd) 

1997–98 

Nutrients Starting Point 

TN 

(mg/L) 

TP 

(mg/L) 

TN 

(lbs/day)

TP 

(lbs/day)

Smurfit-Stone Container 

Corporation 6.88 - 20 8.85 6.8 1.1 502 85 

Jefferson Smurfit – JAX - - 6 6.0 8.8 1.2 441 58 

USN – NS Mayport WWTF 0.88 0.044 2 1.03 3.2 2.1 27 18 

USN – NAS Jacksonville 

WWTF 0.955 0.048 3 1.13 8.5 1.7 80 16 

Georgia-Pacific 24.49 - 40 34.2 5.5 1.4 1556 385 

Jacksonville Beach WWTF 2.5 0.13 4.5 3.2 9.1 2.2 242 59 

Neptune Beach WWTF 0.744 - 1.5 0.94 8.8 1.4 69 11 

Green Cove Springs – Harbor 

Road WWTF 0.514 0.236 0.75 0.75 9.2 2.9 57 18 

Westminster Woods – (Wesley 

Manor Retirement Village) 0.03 - 0.09 0.050 4.6 2.0 1.9 0.83 

Atlantic Beach – Buccaneer 

WWTF 0.91 0.13 1.9 1.13 13.4 1.4 127 13 

JEA – Mandarin WWTF 5.88 1.1 7.5 7.0 5.34 2.3 312 134 

JEA – Monterey WWTF 

(operated by UWF) 2.66 0.94 3.6 3.6 11.3 1.6 341 49 

JEA – Holly Oaks WWTF 

(formerly UWF) 0 0 1 0 8.3 2.1 0 0 

JEA – San Jose WWTF 

(formerly UWF) 1.65 0.60 2.25 2.25 10.0 2.9 188 55 

JEA – Jacksonville Heights 

WWTF (formerly UWF) 1.07 0.43 2.5 1.62 10.1 2.9 136 40 

Orange Park WWTF 1.16 - 2.5 - - 3.7 150 41 

JEA – San Pablo WWTF 

(formerly UWF) 0.58 0.18 0.75 0.75 6.5 3.5 40 22 

CCUA – Miller Street WWTF 3.54 1.46 4.99 4.99 4.5 3.2 189 133 

JEA – Ortega Hills WWTF 

(formerly UWF) 0.09 0 0.22 0 16.8 2.3 0 0 

JEA – Buckman WWTF 32.04 0.96 52.5 34.02 10.5 4.7 2966 1331 

JEA – Arlington WWTF 12.86 5.14 20 18 14.3 2.6 2143 393 

JEA – Northeast WWTF (fka 

JEA - District II WWTF) 3.2 1.05 10 5.4 22.7 5.9 1016 263 

JEA – Southwest WWTF 7.30 4.70 10 10 10.5 1.4 875 116 

JEA – Royal Lakes WWTF 

(formerly UWF) 1.64 0.66 3.25 2.99 7.8 3.8 193 94 

FWSC – Beacon Hills SD 

WWTF 0.66 0.25 1.3 0.99 11.9 2.0 99 16.8 

FWSC – Woodmere SD WWTF 0.43 0.21 0.7 0.64 11.6 1.7 61 8.8 

Green Cove Springs – South 

WWTF 0.21 0 0.5 0.27 13.6 2.3 31 5.3 

CCUA – Fleming Oaks WWTF 0.37 0.03 0.49 0.40 3.0 1.9 10.1 6.5 

Atlantic Beach – Main WWTF 

(D001) 1.73 0.07 3 1.8 11.4 2.1 170 31 

 27 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

1997–98 Starting Starting Point Current Projected Permitted Nutrients Point Name of Facility Flow 

(mgd) 

Increase Flow 

(mgd) (mgd) Flow 

(mgd) 

TN 

(mg/L) 

TP 

(mg/L) 

TN TP 

(lbs/day) (lbs/day)

Palatka WWTF 2.22 0.35 3 3.0 14.7 2.4 367 60 

Anheuser Busch – Main St. – 

Land Application 1.46 - 2.6 2.6 3.9 0.3 84 7.6 

Hastings WWTF 0.085 0.018 0.12 0.103 4.5 0.6 3.9 0.53 

JEA – Julington Creek Creek 

WWTP 0.21 2 0.476 0.476 12.0 3.0 48 12 

CCUA – Fleming Island WWTF 

(combined) 1.078 - 6.365 - - - 172 64 

UWF – Saint Johns North 

WWTF - 0 - 0 6.5 1.7 0 0 

Brierwood SD – Beauclerc STP - 0 - 0 - - 0 0 

Seminole Electric Cooperative, 

Inc., Palatka Plant 7.46 - 346 - 

 28 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

6. DETERMINATION OF THE TMDL 

6.1 Expression and Allocation of the TMDL 

The objective of a TMDL is to provide a basis for allocating acceptable loads among all of the 

known pollutant sources in a watershed so that appropriate control measures can be 

implemented and water quality standards achieved. A TMDL is expressed as the sum of all 

point source loads (wasteload allocations, or WLAs), nonpoint source loads (load allocations, or 

LAs), and an appropriate margin of safety (MOS), which takes into account any uncertainty 

concerning the relationship between effluent limitations and water quality: 

TMDL = ∑ WLAs + ∑ LAs + MOS

As mentioned in Section 4.1, the WLA is broken out into separate subcategories for wastewater 

discharges and stormwater discharges regulated under the NPDES Program: 

TMDL ≅ ∑ WLAswastewater + ∑ WLAsNPDES Stormwater + ∑ LAs + MOS 

It should be noted that the various components of the revised TMDL equation may not sum up 

to the value of the TMDL because (1) the WLA for NPDES stormwater is typically based on the 

percent reduction needed for nonpoint sources and is accounted for within the LA, and (2) 

TMDL components can be expressed in different terms (for example, the WLA for stormwater is 

typically expressed as a percent reduction, and the WLA for wastewater is typically expressed 

as mass per day). 

WLAs for stormwater discharges are typically expressed as “percent reduction” because it is 

very difficult to quantify the loads from MS4s (given the numerous discharge points) and to 

distinguish loads from MS4s from other nonpoint sources (given the nature of stormwater 

transport). The permitting of stormwater discharges is also different than the permitting of most 

wastewater point sources. Because stormwater discharges cannot be centrally collected, 

monitored, and treated, they are not subject to the same types of effluent limitations as 

wastewater facilities, and instead are required to meet a performance standard of providing 

treatment to the “maximum extent practical” through the implementation of BMPs. 

This approach is consistent with federal regulations (40 CFR § 130.2[I]), which state that TMDLs 

can be expressed in terms of mass per time (e.g., pounds per day), toxicity, or other 

appropriate measure. TMDLs for the LSJR are expressed in terms of kilograms per year, and 

represent the maximum annual TN and TP load the freshwater and estuarine reaches of the 

river can assimilate and maintain the narrative nutrient criterion (Tables 5 and 6). As described 

in the note for Tables 5 and 6, a daily expression of the TMDLs can be calculated by dividing 

the annual average load by 365.25. The resultant loads represent the total maximum annual 

average daily loads. However, the TMDLs to be implemented are those expressed on a mass 

per year basis, and the expression of the TMDL on a mass per day basis is for information 

purposes only. As noted in Section 5.5, the TMDL for the estuarine portion of the river is for TN 

only because nitrogen is the limiting nutrient for this portion of the river. 

Appendix J provides the allocation to specific wastewater facilities. The division of the 

available assimilative capacity between the WLA and LA was determined using information 

 29 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

about individual sources and source categories. The allocation methodology followed the 

recommendations in the 2001 Report to the Governor and Legislature on the Allocation of Total 

Maximum Daily Loads (Department, 2001), with site-specific revisions to the allocation 

methodology recommended by the LSJR TMDL Executive Committee. Under this approach, 

initial reductions for the river were targeted at nonpoint source loads assuming the 

implementation of BMPs. As BMP implementation alone did not result in sufficient reductions, 

all anthropogenic sources, including the upstream load, were reduced by the same percentage 

until the assimilative capacity was met, except that that prior treatment or prior commitments in 

treatment improvements was taken into account for individual point sources. 

For the case of domestic wastewater facilities in the marine portion of the river, the allocations 

are based on their starting point flow and a target TN concentration of 5.4 mg/L. Using this 

approach, facilities that already provided advanced waste treatment (typically defined as a TN of 

3 mg/L) did not have to make additional reductions, and in fact could increase their discharged 

load or generate credits. 

Allocation calculations were conducted using an Excel spreadsheet, and Appendix J provides 

table versions of the spreadsheets used to allocate loadings in the freshwater and estuarine 

portions of the river (interested parties can request an electronic copy of the spreadsheet if they 

would like to see spreadsheet formulas). 

Table 5. TMDL Components for the Freshwater Portion of the LSJR 

WBIDs Parameter TMDL

(kg/yr) 

WLA3

(kg/yr) 

LA 

(kg/yr) MOS

2213I to 2213N Total Nitrogen 8,571,563 236,695 8,334,868 Implicit 

2213I to 2213N Total Phosphorus 500,325 46,357 453,968 Implicit 

Table 6. TMDL Components for the Estuarine Portion of the LSJR 

WBIDs Parameter TMDL

(kg/yr) 

WLA

(kg/yr) 

LA

(kg/yr) MOS

2213A to 2213H Total Nitrogen 1,376,855 1,027,590 349,265 Implicit 

Note: To calculate the total maximum annual average daily load that should be expected, divide the annual average load by 

365.25. 

It should be noted that some facilities requested that the Department combine their WLAs into 

an aggregate WLA to allow flexibility, so that reductions from one facility can be shifted to 

another as long as the net reduction reaches the aggregate WLA. For these aggregate 

allocations, the Department plans to issue watershed permits that will require compliance with 

the aggregate WLA. 

 

3

 As described in Section 6.2, this WLA includes a percent reduction in current loading from sources covered by the NPDES 

Stormwater Program. 

 30 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

6.2 Load Allocations 

The LA for the freshwater portion of the LSJR includes the following loads: (1) the natural 

background nonpoint source load (which includes background upstream loads from the Middle 

St. Johns River [MSJR] and background loads from Dunns Creek); (2) augmented nonpoint 

source loads (again including augmented upstream loads from the MSJR and Dunns Creek); 

and (3) atmospheric deposition. To determine the allocation between the WLA and LA, the 

augmented TN and TP nonpoint source loads were first reduced by the amounts estimated for 

the implementation of applicable BMPs on agricultural lands and urbanized areas, and then 

augmented nonpoint sources (excluding atmospheric deposition) and point sources were 

reduced by the same percentage until the assimilative capacity was met. Using this approach, 

the LA takes into account reductions expected in the upstream load from the MSJR. It should 

also be noted that the LA includes loading from stormwater discharges regulated by the 

Department and the water management districts that are not part of the NPDES Stormwater 

Program (see Appendix E). 

Appendix J provides allocations of urban nonpoint source loads to individual jurisdictions in the 

freshwater portion of the river. These allocations were developed in the same manner as for 

MS4s (see Appendix M) and were expressed as percent reductions rather than load. 

The load allocation for the marine portion of the river was developed in the same manner as for 

the freshwater portion. Allocations to individual jurisdictions (shown in Appendix J) were 

expressed as percent reductions. 

6.3 Wasteload Allocations 

The WLA for the estuarine portion of the river is a combination of the sum of the WLAs for all of 

the NPDES wastewater facilities and the stormwater discharges from the MS4 jurisdictions 

(Appendix J). As noted in Section 6.1, the TMDLs to be implemented are those expressed on 

a mass per year basis, and effluent limits for wastewater discharges to the river will be based on 

the annual expression. While the loads for individual MS4s were calculated, the allocations to 

the MS4s are expressed as a percent reduction rather than loads. Appendix M describes the 

methodology to determine the required percent reduction in urban stormwater for each MS4 

discharging to the estuarine portions of the river. 

The WLA for the freshwater portion of the river is the sum of the WLAs for all of the NPDES 

wastewater facilities and a percent reduction assigned to stormwater discharges subject to the 

Department’s NPDES Stormwater Program. As with the marine portion of the river, allocations 

to each MS4 in the freshwater portion of the river are expressed as a percent reduction. 

It should be noted that any MS4 permittee is only responsible for reducing the loads associated 

with stormwater outfalls that it owns or otherwise has responsible control over, and it is not 

responsible for reducing other nonpoint source loads in its jurisdiction. 

6.4 Aggregate Loads and Pollutant Trading 

Some facilities requested that the Department combine their WLAs into an aggregate WLA to 

allow flexibility in how they meet the required load reductions. While this aggregation was 

straightforward for entities with multiple wastewater facilities, the aggregation was slightly more 

 31 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

complex for municipalities that wanted to aggregate their wastewater and MS4 allocations, 

because the allocations to MS4s were expressed as percent reductions. The approach was to 

simply convert the percent reduction back into a load using the loading in the allocation 

spreadsheet. 

This approach clearly works for the TMDL for the freshwater portion of the river, which is based 

on a long-term average condition (based on the chlorophyll a target of not exceeding 40 ug/L 

more than 10 percent of the time). This approach also works in the marine portion of the river, 

even though the TMDL is based on a dry year (1999 was the worst-case year for DO, when 

tributary flows were low, nutrients were concentrated in the river due to less dilution, and 

residence times were longer). Model runs4

 indicate that the percent reductions needed in other 

model years are about half of the reductions in 1999 (a 15 percent reduction required in 1996 

and 1997, compared with a 28.5 percent reduction required in 1999), while the urban 

stormwater loads for these years are less than twice the 1999 load. As such, it is adequately 

protective to use the 1999 load for aggregation purposes. 

For the aggregate allocations, the Department plans to issue watershed permits that will require 

compliance with the aggregate WLA. These permits will be in addition to the facilities’ current 

permits, and will focus on compliance with the WLA. 

This approach of converting the percent reduction back into the allowable load for 1999 is also 

applicable if MS4s decide to meet their required reductions through water quality credit trading. 

The WLAs given to point sources can be modified via trading as long as the overall load does 

not exceed the TMDL. The combined WLA (both total and facility-specific) is provided to allow 

flexibility so that reductions from one discharger can be shifted to another as long as the net 

allocation achieves the TMDL. The Department plans to address the permitting process and 

requirements for water quality credit trading, including trading factors, in the Basin Management 

Action Plan (BMAP) for the TMDL. 

6.5 Margin of Safety 

Consistent with the recommendations of the Allocation Technical Advisory Committee 

(Department, 2001), an implicit MOS was assumed in the development of this TMDL. An 

implicit MOS was provided by the conservative decisions associated with a number of modeling 

assumptions, the development of site-specific alternative water quality targets, and the 

development of assimilative capacity. 

In the freshwater zone, multiple years of phytoplankton and zooplankton field measurements 

were evaluated to establish the site-specific chlorophyll a level beyond which zooplankton 

abundance and diversity started to decline. Hydrodynamic/water quality simulations over four 

different years were then evaluated to determine the appropriate long-term average TN and TP 

load reductions necessary to meet the chlorophyll a target. These four years represent flows 

that were slightly drier than average conditions and, given that the effects of nutrient impairment 

are more prominent in dry conditions, this long-term, yet dry period is considered conservative. 

The expression of the TMDL also provided an implicit MOS because equal percent reductions of 

both TN and TP were required, even though both nutrients may not be the limiting factor for a 

 

4

 These model runs were evaluated because the Department was concerned that the amount of load aggregated, if based on the 

dry year loading, could conceivably be inadequately protective during wetter years when MS4 loads would be higher, depending on 

the percent reduction required for the wetter years. 

 32 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

given year in the freshwater zone. In addition, reductions were based on meeting the target 

within all five WBIDs in the freshwater zone. As such, the “worst-case” WBID controlled the 

amount of reduction needed. Finally, point source flows and loads used in the WLA for the 

freshwater zone were based on existing flows and loads with an allowance for growth rather 

than assuming permitted limits. This approach provides an implicit MOS because it is extremely 

unlikely that all of the point sources would simultaneously discharge at their full WLA. 

Conservative assumptions were also part of the development of the TMDL for the oligohaline/ 

mesohaline portion of the river. As in the freshwater zone, four different years were simulated. 

However, in this case, the worst-case year (1999) was used to establish necessary nitrogen 

load reductions in the oligohaline/mesohaline zone because the controlling factor, DO, can 

result in impairment in shorter time frames than increased algal biomass. In 1999, there were 

reduced rainfall and increased residence times, which resulted in reduced DO levels and a large 

fish kill. As in the freshwater zone, the percent reduction needed for the oligohaline/mesohaline 

zone was based on ensuring that the target was met in all of the WBIDs in these zones. 

Another conservative assumption involved the methodology used to establish the DO SSAC in 

the marine portion of the river. For example, a minimum DO of 4.0 mg/L was specified and 

certain conservative assumptions were made regarding larval recruitment and growth in the 

development of the SSAC. 

Finally, point source flows and loads used in the WLA for the oligohaline/mesohaline zones 

were based on existing flows and loads with an allowance for growth rather than assuming 

permitted limits. As noted previously, this approach provides an implicit MOS because it is 

extremely unlikely that all of the point sources would simultaneously discharge at their full WLA. 

6.6 Seasonal Variability 

Seasonal variability was assessed during the development of this TMDL as part of the 

development of the site-specific water quality targets and the determination of assimilative 

capacity. The site-specific targets developed for the freshwater and oligohaline/mesohaline 

zones account for the seasonal cycles in algal growth. In the freshwater zone, the critical period 

occurred from April through August, when excessive algal growth led to imbalances in the algal 

community structure (dominance by only a few species) and impacts to the food web 

(undesirable prey for zooplankton and fish species). The chlorophyll a target for the freshwater 

zone (40 μg/L not to be exceeded more than 10 percent of the time) was specifically designed 

to prevent algal blooms of sufficient duration to cause these imbalances in flora and fauna in the 

future. 

The TMDL for the oligohaline/mesohaline zone also accounted for seasonal variability. As 

discussed earlier in the MOS section, the summer of 1999 was a critical period, during which 

DO was below 4.0 mg/L at levels and for durations that could adversely impact the aquatic 

fauna in the oligohaline/mesohaline zones. The method used to develop the DO target 

accounts for these critical, seasonal (and diurnal) periods and ensures that excursions of DO 

levels below the chronic threshold will not occur at a magnitude or duration that would result in 

impacts to aquatic fauna. 

 33 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

7. NEXT STEPS: IMPLEMENTATION PLAN 

DEVELOPMENT AND BEYOND 

7.1 Basin Management Action Plan 

Following the adoption of the TMDL by rule in 2004, the LSJR TMDL Executive Committee 

continues to meet and provide input on a more detailed allocation. These efforts will be 

reflected in the BMAP for the LSJRB, which is currently scheduled for adoption in summer 2008. 

The BMAP will include the following: 

• Appropriate allocations among the affected parties; 

• A description of the load reduction activities to be undertaken; 

• Timetables for project implementation and completion; 

• Funding mechanisms that may be utilized; 

• Any applicable signed agreements; 

• Local ordinances defining actions to be taken or prohibited; 

• Local water quality standards, permits, or load limitation agreements; and 

• Monitoring and follow-up measures. 

TMDL development and implementation is an iterative process, and this TMDL will be reevaluated during the BMAP development process and subsequent watershed management 

cycles. The Department recognizes that it may be appropriate to revise the TMDL in the future 

when more information has been collected and analyzed. 

With such possible revisions in mind, this TMDL is characterized as an adaptive management 

TMDL, in which the Department uses the best available information at the time to develop the 

TMDL. However, the adaptive management approach recognizes that additional data and 

information may be necessary to validate the assumptions of the TMDL, and that the additional 

information should be pursued to improve the next iteration of the TMDL 

One of the key issues that determined the allowable loading for this TMDL was the 

Department’s interpretation of the narrative nutrient criterion for the water quality target (40 ug/L 

not to be exceeded more than 10 percent of the time) for the TMDL. Given the importance of 

the water quality target, the Department plans to work with stakeholders to conduct monitoring 

of the river (see Section 3.3) designed to further evaluate the water quality target for nutrients 

and to determine the effectiveness of the pollution control activities required by this TMDL. 

It should also be noted that this TMDL does not directly address nutrient impacts on SAV. The 

Department and the SJRWMD agree that the TMDL would ideally address nutrient impacts on 

the SAV community in the LSJR. In fact, one of the reasons the CE-QUAL-ICM model was 

selected for this TMDL was that it had the capability to simulate SAV, including epiphytic growth 

effects on SAV. 

 34 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

 35 

Florida Department of Environmental Protection 

However, specific studies of the effects of nutrients, light, and salinity on the dominant SAV 

species in the LSJR were not completed in time to allow for the SAV modeling component of 

CE-QUAL-ICM to be used for this version of the TMDL. The SJRWMD is actively pursuing 

these studies and they should be completed over the next two years (see Appendix K for a list 

of ongoing and proposed studies that will provide the necessary information to model SAV 

response). 

As this information becomes available, the model code will be revised to incorporate a sitespecific light model and additional state variables that influence SAV growth, and the model will 

be recalibrated for use in the next iteration of the TMDL. If there are any changes in the 

estimate of the assimilative capacity as a result of the revisions to the water quality target or 

model code to address SAV, the rule adopting this TMDL will be revised, providing a point of 

entry for interested parties. 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

 36 

Florida Department of Environmental Protection 

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Bricker, S.B, C.G. Clement, D.E. Pirhalla, S.P. Orlando, and D.R.G. Farrow. September 1999. 

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estuaries. Silver Spring, Maryland: National Oceanic and Atmospheric Administration, 

National Ocean Service, Special Projects Office and the National Centers for Coastal Ocean 

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Burkholder, J.M., and H.B. Glasgow, Jr. 1997a. Pfiesteria piscicida and other Pfiesteria-like 

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Burkholder, J.M., and H.B. Glasgow, Jr. 1997b. Trophic controls on stage transformations of a 

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Cerco, C., and T. Cole. 1993. Three-dimensional eutrophication model of Chesapeake Bay. 

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———. February 2001. A report to the Governor and the Legislature on the allocation of Total 

Maximum Daily Loads in Florida. Tallahassee, Florida: Bureau of Watershed Management. 

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Fisher, D.C., and M. Oppenheimer. 1991. Atmospheric nitrogen deposition and the 

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Floyd, S.S., E.M. Irwin, and D.A. Evans (Eds.). 1997. Florida statistical abstract. University of 

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Greening, H., L.K. Dixon, A. Squires, P. Hessling, T. D’Aquila and T. Rogers. 1997. 

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Hamrick, J.M. 1992. A three-dimensional environmental fluid dynamics computer code: 

Theoretical and computational aspects. Special Report 317. Gloucester, Virginia: College 

of William and Mary, Virginia Institute of Marine Science. 

Hendrickson, J., and J. Konwiniski. 1998. Seasonal nutrient import-export budgets for the 

Lower St. Johns River, Florida. St. Johns River Water Management District. 

Hendrickson, J., and W. Magley. 2001. Development of total maximum daily loads and 

pollutant load reduction goals for the Lower St. Johns River Basin: Plan of study. St. Johns 

River Water Management District. 

Hendrickson, J., N. Trahan, E. Stecker, and Y. Ouyang. 2004. Estimation and assessment of 

the current and historic external load of nitrogen, phosphorus and organic carbon to the 
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Florida Department of Environmental Protection 

Lower St. Johns River for the fulfillment of TMDL and PLRG objectives. Palatka, Florida: 

St. Johns River Water Management District, Department of Water Resources. 

Hendrickson, J.C., E.F. Lowe, D. Dobberfuhl, P. Sucsy, and D. Campbell. 2003. 

Characteristics of accelerated eutrophication in the Lower St. Johns River Estuary and 

recommended targets to achieve water quality goals for the fulfillment of TMDL and PLRG 

objectives. Palatka, Florida: St. Johns River Water Management District, Department of 

Water Resources. 

Janicki, A., and G. Morrison. 2000. Developing a Trophic State Index for Florida’s estuaries. 

Submitted to the Florida Department of Environmental Protection. St. Petersburg, Florida: 

Janicki Environmental, Inc. 

Paerl, H.W. 1993. Emerging role of atmospheric nitrogen deposition in coastal eutrophication: 

Biogeochemical and trophic perspectives. Can. J. Fish. Aquat. Sci. 50: 2254-2269.

Phlips, E.J., M. Cichra, F.J. Aldridge, J. Jembeck, J. Hendrickson, and R. Brody. June 2000. 

Light availability and variations in phytoplankton standing crops in a nutrient-rich blackwater 

river. Limnology & Oceanography 45:(4) 916-929. 

Pollman, C.D., and S. Roy. 2003. Examination of atmospheric deposition chemistry and Its 

potential effects on the Lower St. Johns Estuary. Final Report Submitted to the St. Johns 

River Water Management District, Contract No. SE706AA. Gainesville, Florida: Tetra Tech, 

Inc. 

Pribble, R.J., and A.J. Janicki. 1998. Atmospheric deposition contributions to nitrogen and 

phosphorus loadings in Tampa Bay: Intensive wet and dry deposition collection and 

analysis. Report prepared for the Tampa Bay National Estuary Program, St. Petersburg, 

Florida. 

St. Johns River Water Management District. January 1993. SWIM Plan for the Lower St. Johns 

River. Palatka, Florida. 

Sucsy, P.V., and F.W. Morris. 2002. Calibration of a three-dimensional circulation and mixing 

model of the Lower St. Johns River. Technical Memorandum. St. Johns River Water 

Management District. Palatka, Florida. 

Sucsy, P., and J. Hendrickson. 2004. Calculation of nutrient reduction goals for the Lower St. 

Johns River by application of CE-QUAL-ICM, a mechanistic water quality model. Palatka, 

Florida: St. Johns River Water Management District, Department of Water Resources. 

Tillman, D., C. Cerco, M. Noel, J. Martin, and J. Hamrick. 2004. Three-dimensional 

eutrophication model of the Lower St. Johns River, Florida. ERDC/EL TR-04-13. Vicksburg, 

Mississippi: U.S. Army Engineer Research and Development Center. 

U.S. Environmental Protection Agency. September 1999. Ambient water quality criteria for 

dissolved oxygen (salt water): Cape Cod to Cape Hatteras. EPA 822-D-99-002. 

Washington, D.C.: Office of Water, Office of Science and Technology. 

———. October 2001. Nutrient criteria technical guidance manual: Estuarine and coastal 

marine waters. EPA 822-B-01-003. Washington, D.C.: Office of Water. 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix A: The LSJR TMDL Executive Committee 

This broad-based group, convened by the Department’s Northeast District, has been meeting 

since July 2002. It has advised the Department on issues such as water quality targets and 

allocation processes. The committee will play a critical role in the development of the BMAP to 

implement TMDLs. The committee membership as of July 2003 is listed below. 

LSJR TMDL Executive Committee 

Interest Group Representative 

Florida Department of Environmental 

Protection Mario Taylor, Northeast District (Chair) 

Industry Mike Burch, Plant Manager, Rayonier 

Agriculture Wayne Smith, President, North Florida Growers Exchange 

Builders Neil Aikenhead, Northeast Florida Builders Association 

Utility Authorities Susan Hughes, JEA 

Environmental Interest Groups Roger Bass, St. Johns Riverkeeper 

Don Loop, Stewards of the St. Johns River 

Regional Planning Council Brian Teeple, Northeast Florida Regional Planning 

Council 

Forestry Jim Kuhn, Shadow Lawn Farms 

Local Government Honorable Glen Lassiter, Clay County Commission 

Florida Department of Agriculture and 

Consumer Services Jody Lee 

MSW – Public Works Ed Hall, City of Jacksonville Public Works 

St. Johns River Water Management District Casey Fitzgerald (for Executive Director Kirby Green) 

U.S. Army Corps of Engineers Richard Bonner 

LSJR Executive Committee Mission Statement 

The LSJR TMDL Executive Committee advises the Department on the development and 

implementation of TMDLs for the basin. The committee represents and communicates with key 

stakeholders to secure local input and consensus on pollutant reductions. The committee is 

charged with recommending a “reasonable and equitable” allocation of pollutant load reductions 

for achieving TMDLs in the lower basin and, in conjunction with the Department, developing a 

BMAP to implement those load reductions. 

 38 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix B: Eutrophication Defined 

Eutrophication is generally described as a process of changing the ecological status of a 

waterbody by increasing the baseline (e.g., primary) level of productivity, almost invariably as a 

result of increasing nutrient supply. Some researchers (Nixon, 1995) have suggested that 

estuarine eutrophication be defined as “an increase in the rate of supply of organic matter to an 

ecosystem,” as the effect of eutrophication in most systems is an increase in plant (algae and/or 

nuisance aquatic plants) biomass. 

The general sequence of eutrophication effects is as follows. In the enrichment phase, there is 

an episodic or continuous increase in algal and plant biomass. Above a certain level of nutrient 

availability, changes in plant species composition occur that can have profound effects on the 

habitat and structure of the rest of the food web, potentially affecting energy flow in the entire 

ecosystem. Secondary effects can include reductions in light penetration that can reduce the 

species composition and depth distribution of benthic plants, the increased probability of the 

occurrence of toxic/nuisance phytoplankton blooms, hypoxia (commonly used to describe DO 

concentrations at or below 2.0 mg/L), and behavioral effects on other organisms in the food web 

(Gray, 1992). Extreme effects can include the mass growth of undesirable plants, regular 

blooms of toxigenic and other nuisance algae, and, ultimately, the migration or mortality of 

various species. 

 39 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix C: Basis for LSJR Water Quality Targets 

(Excerpts5 from Hendrickson et al., 2003, Characteristics of Accelerated Eutrophication 

in the Lower St. Johns River Estuary and Recommended Targets to Achieve Water 

Quality Goals for the Fulfillment of TMDL and PLRG Objectives) 

 

Water Quality Targets for the LSJR 

Some measure of the three most commonly identified water quality effects of estuarine 

eutrophication—nuisance levels of algal biomass, reduced dissolved oxygen and reduced 

transparency—were recommended in the original Plan of Study (POS) document as the 

response variables in establishing nutrient TMDLs and PLRGs for the LSJR. These TMDL and 

PLRG targets were originally established consistent with standards or thresholds set forth in 

Chapter 62-302, F.A.C., and Chapter 62-303, F.A.C. However, in the process of data analysis 

and investigation to describe nutrient enrichment effects and to quantify these relationships 

through water quality modeling, these targets have undergone refinement in order to more 

closely address the most problematic aspects of eutrophication in the LSJR. 

Relevant questions driving the re-definition of targets were: 

1. Is the dissolved oxygen State standard sufficiently protective, or conversely, 

unnecessarily protective, for biota endemic to the LSJR? 

2. Is the maintenance of transparency, based upon open water changes in 

compensation depth, relevant to SAV colonization in the LSJR? 

3. Do algal biomass targets, based upon mean annual chlorophyll a concentrations, 

sufficiently address the most problematic aspects of nuisance algal blooms? 

Because of the weak linkage between open water, planktonic algal attenuation that is embodied 

in the transparency standard as stated in Chapter 62-302, F.A.C., and the more realistic case of 

epiphytic algal attenuation for littoral submerged grasses, it was felt that the transparency 

criteria is not the appropriate target for protection of SAV in the LSJR. Investigations relating 

nutrient enrichment effects to SAV health, and the interactions between natural factors of light, 

color and substrate and nutrient enrichment are ongoing and can be used to revise the LSJR 

nutrient TMDL if warranted. 

In light of the great amount of research in support of oxygen criteria, and the recent work 

accomplished in compiling and refining this research in EPA’s Ambient Aquatic Life Water 

Quality Criteria for Dissolved Oxygen (Saltwater): Cape Cod to Cape Hatteras, it was felt that 

sufficient effort could not be mustered, nor was warranted, to refute these recommendations for 

the LSJR TMDL. Therefore, methodologies provided in this guidance have been relied upon 

5

 Text provided is from the DRAFT available at the time the TMDL was adopted. Readers should refer to the referenced document 

for more up-to-date text. Only text was excerpted. Figures and tables referenced in the text are available in the final document and 

may be obtained from the SJRWMD. 

 40 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

for establishing algal biomass targets for the predominantly marine reach of the river. While 

these methods apply a less restrictive criteria for maintenance of aquatic life based on dissolved 

oxygen than the current Florida Water Quality Standard, they are arguably more realistic given 

the natural stressors to oxygen level in a southern temperate blackwater river estuary. 

And finally, as experimental evidence suggests that the greatest level of harm from algal blooms 

occurs from extreme bloom events, the chlorophyll a targets for the LSJR were redefined to 

emphasize the reduction of high concentration and long duration events. 

LSJR Freshwater Phytoplankton Community Composition 

Dynamics and Zooplankton Interactions 

The fundamental objective for LSJR TMDL and PLRG nutrient load reduction modeling was the 

enhancement of plankton ecology for both freshwater and marine environments. This approach 

was taken because 1) the LSJR is largely a plankton based system, with the majority of its 

autochthonous carbon produced through phytoplankton primary production, and 2) a large 

database composed of five years of phytoplankton and zooplankton monitoring data exists for 

the LSJR, representing the most powerful biological evaluation tool available. 

For the freshwater river, three elements of plankton ecology were assessed: 

1) What maximum levels of algal biomass maintain diversity in the plankton 

community? 

2) What maximum levels of algal biomass, or what phytoplankton community 

composition, facilitates the upward transfer of planktonic primary production to 

higher trophic levels? 

3) What levels of algal biomass minimize the potential for the expansion of 

detrimental algal species or the production of algal toxins? 

Freshwater LSJR Algal Biomass Target 

Maintenance of Phytoplankton Diversity 

The maintenance of organism diversity is a fundamental goal of biological restoration. Diversity 

in biological systems promotes stability; conversely, ecosystems with narrow species diversity 

are prone to large perturbations in communities. The loss of phytoplankton diversity, and the 

dominance of cyanobacteria during the spring and summer growth seasons is one of the most 

conspicuous aspects of freshwater blooms of the LSJR. As total phytoplankton community 

biomass (expressed as chlorophyll a) increases, the fraction of the total community biomass 

composed of blue-greens (determined from biovolume estimates) increases (Figure 27). Blue 

green relative composition is variable and often low for chlorophyll a concentrations to about 40 

mg/m3

. After this point, blue green biomass represents the majority of phytoplankton community 

composition. At chlorophyll a concentration above 60 mg/m3

, blue green relative abundance is 

regularly between 80 to 90 percent. 

 41 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Facilitation of Upward Trophic Transfer of Primary Production 

In its Chesapeake Bay Water Quality Criteria Guidance Manual, EPA outlines an approach to 

the development of chlorophyll a criteria for the purpose of enhancing the upward transfer of 

phytoplankton carbon to the zooplankton community. The conceptual model utilized in the 

Chesapeake Bay (CB) Guidance relating mesozooplankton response to increases in algal 

biomass is depicted in Figure 28. This model is based on the premise that at low to moderate 

phytoplankton densities, zooplankton populations respond favorably and increase with increase 

in algal biomass associated with increase in food supply. At some point, however, the increase 

in toxic or otherwise unpalatable taxa in the phytoplankton community, and an increase in 

feeding effort due to the density of unfavorable species, leads to a leveling off and perhaps even 

decline in the desirable zooplankton. The point of the departure from the linear increase in 

zooplankton – phytoplankton biomass represents the maximum desirable algal biomass. 

Plankton monitoring data (Nov. 1996 through Oct. 2001) were examined to determine if a 

relationship similar to that described above existed for the freshwater LSJR. The zooplankton – 

algal biomass relationship is shown in Figure 29. Desirable zooplankton in these graphs are 

estimated by summing the organism counts for copepods and cladocerns only. Rotifers are 

excluded, as they are believed to be feeding on small detrital particles and bacteria, and are not 

believed to be as important a group of zooplankters in supporting the upward transfer of carbon 

to the fish community. Although a good deal of spread exists in this graph in zooplankton 

abundance at low to moderate chlorophyll a concentration, it is possible to discern a pattern that 

matches the conceptual model forwarded by the CB guidance. 

This graph suggests that the linear increase in zooplankton abundance with increasing 

chlorophyll a concentration begins to decline somewhere between chlorophyll a concentrations 

of 40 to 60 mg/m3

. The adverse response of zooplankton numbers to high levels of algal 

biomass can be seen in Figure 29 for the specific case of the severe algal blooms that occurred 

at Racy Point in 1999. At this station, zooplankton numbers increase initially as chlorophyll 

concentration increases, but then decline as chlorophyll continues to increase. This pattern is 

repeated for the year’s second bloom, which peaks in late August. 

Algal Toxin Formation Potential 

In recently completed work, Paerl and Charmichael (2002) examined levels of the algal toxins 

microcystin, anatoxin, and cylindrospermopsin in nutrient enrichment assays performed on 

LSJR samples collected from October 2000 through August 2001. All toxins were detected 

during the sampling, with microcystin present in every assay. Microcystin was found to be 

positively correlated to chlorophyll a (e.g., algal biomass), and this relationship is shown in 

Figure __. Generally, microcystin levels remained low for chlorophyll a concentrations below 40 

μg/L. Above this level, microcystin levels were found to be variable, but on occasion reached 

very high levels, near the World Health Organization standard for drinking water of 1 μg/L. The 

LSJR is not a drinking water source, and relevance of this standard for the protection of aquatic 

life has not been quantified. However, the result of these assay experiments suggests that at 

concentrations of chlorophyll a that exceed 40 μg/L, the potential for the appearance of 

microcystin in ambient water increases greatly. 

 42 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Algal Bloom Duration 

Plankton monitoring data and algal toxin assays indicate that blue green algal blooms of the 

LSJR freshwater reach begin to exhibit detrimental effect as bloom biomass, measured as 

chlorophyll a, exceeds 40 mg/m3

. These effects would not be expected to be instantaneous at 

concentrations above 40 mg/m3, but instead to require some level of duration and intensity. 

When the numbers of copepods and cladocerans (again, considered to be an indicator of 

beneficial zooplankton) in plankton sampling are compared to the durations of above 40 mg/m3

chlorophyll a excursions (Figure 30), it can be see that as durations exceed 40 days, copepods 

and cladoceran numbers are noticeably reduced. In the duration analysis of Figure 10, between 

20 to 45 percent of blooms within the freshwater reach exceeded this duration. 

The mean duration of above 40 mg/m3

 episodes is between 20 to 30 days within the freshwater 

reach (Figure 10), but bloom duration increases disproportionately as blooms exceed 30 days. 

For example, the increase in duration from the 40th percentile bloom to the 50th percentile is 

approximately 10 days, while the increase from the 50th to the 60th percentile event is on the 

order of 20 days. When the maximum concentration of blooms is compared to the bloom 

duration (Figure 31), the maximum concentrations (based on the linear regressions) 

corresponding to 40-day durations range between 50 to 74 mg/m3

 chlorophyll a. Using the 

Racy Point station data, it is possible to parameterize a new distribution of chlorophyll a that 

hypothetically would meet the conditions for the maintenance of phytoplankton and zooplankton 

diversity. This was done by proportionally scaling the synthesized statistical distribution of the 

existing data (shown in Figure 32 by the dark navy blue line; the natural log of chlorophyll a is 

used to normalize the distribution) to form a new distribution (Figure 32 light blue line) for which 

the 1 percentile occurrence was the same as the observed data, and the 99th percentile 

occurrence (p = 0.01 for a one tailed test) was equivalent to a chlorophyll a of 74 mg/m3

. This 

synthesized distribution had a mean of 20.1 mg/m3

, a variance of 0.56 mg/m3, and a 10.6 

percent occurrence rate for chlorophyll a concentrations greater than 40 mg/m3

. 

Marine LSJR Dissolved Oxygen Targets 

Dissolved Oxygen Effects 

As demonstrated in the previous section outlining eutrophication effects, low dissolved oxygen 

excursions (persistent episodes below the State criteria of 5 mg/L) occur in both the freshwater 

and oligo/mesohaline reaches of the LSJR. These excursions occur coincident with high 

summertime temperatures, and appear to be associated with the decline or crash of significant 

algal blooms, and on an inter-annual basis are correlated with mean spring-summer algal 

biomass levels. The improvement of the dissolved oxygen regime for the river and estuary was 

one of the originally stated objectives of the TMDL and PLRG plan for the river, and the State 

standard of 5 mg/L (instantaneous for freshwater reaches, and as a daily average for 

predominantly marine reaches) was identified as the target on which to base nutrient reduction 

scenario modeling. Even at the time of the proposition of this target, however, considerable 

uncertainty existed regarding its appropriateness and achievability. Low dissolved oxygen 

episodes have long been known to occur in southeast U.S. estuaries (Schroeder and Wiseman, 

1988), and naturally low dissolved oxygen concentrations are known to be a feature of 

blackwater river systems. For these reasons, effort has been directed toward refining oxygen 

regime targets that are based upon the minimum levels necessary for the protection of native 

estuarine aquatic communities. 

 43 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

As an alternative to the fixed standard of 5 mg/L, the procedure described in the recently 

published U.S. Environmental Protection Agency Guidance, Ambient Aquatic Life Water Quality 

Criteria for Dissolved Oxygen (Saltwater): Cape Cod to Cape Hattaras, (U.S. EPA, 200) has 

been used to define the dissolved oxygen target on which reductions of nutrient enrichment 

effects are to be based. The Guidance contains several elements that offer superiority over the 

oxygen standard of F.A.C. 62-302. First, it is based upon the tolerance of low oxygen by 

estuarine fish and invertebrates, as opposed to both fresh and saltwater species. Second, the 

Guidance establishes an absolute minimum oxygen level for the protection of most estuarine 

species against acute low concentrations that result in organism mortality, and distinguishes this 

level from a sub-lethal range that results in reductions in growth and recruitment, and with this, 

presumably fish health and survival probability. Fish community effects within this sub-lethal 

range are based upon the intensity and duration of hypoxic events. Third, the Guidance offers 

approaches for assessing effects of two common types of low dissolved oxygen common to 

eutrophic estuaries: persistent, low dissolved oxygen associated with late season algal bloom 

decline; and diurnal patterns of low oxygen associated with high algal standing stock 

photosynthesis and respiration cycles or tidal transport of low oxygen water masses. In the 

LSJR, the most common and severe low oxygen episodes are long term, persistent events 

associated with late season algal community decline, and the Guidance procedure for 

assessing these types of events has been used to define oxygen targets. 

Organism Acute Oxygen Levels 

The data set used in the Guidance to develop criteria minimum concentration (CMC) was 

assimilated from previous studies that examined species or genus-specific survival under 

continuous low dissolved oxygen exposures. These studies covered 12 invertebrate and 11 fish 

estuarine species, mostly at juvenile life stages. The Florida Marine Research Institute’s 

Fisheries Independent Monitoring Program (FMRI, 2002) has confirmed the presence of five of 

these species in the northeast Florida region (includes one site in the St. Mary’s River, one in 

the Nassau, and 3 in the lower St. Johns estuary), and these are listed in Table 4. Because the 

FMRI sampling is performed using river seines, haul seines and otter trawls, some benthic 

invertebrate species may be under-reported. A trend is evident between the numbers of 

individuals of a given species present in the FMRI sampling, and their low oxygen LC50, in that 

as an individual species low dissolved oxygen tolerance decreases, its abundance declines in 

the northeast Florida sampling region (Figure 33). A numbers of factors could account for this, 

including species natural ranges, sampling methodology, migration patterns or competitive 

interactions, though the possibility that these species are excluded due to prevailing low 

dissolved oxygen, either as a natural occurrence or through accelerated eutrophication, should 

be considered as a contributing factor. 

Following the procedure established in the development of toxics criteria, the CMC is 

determined by adjusting upward LC50 data to estimate the LC5 concentration, using the mean 

LC5/LC50 ratio for all studies, applied to the most sensitive species mean acute value (SMAV). 

In the studies compiled in the Guidance, pipe fish (Syngnathus fuscus), exhibited the highest 

SMAC, at an LC50 concentration of 1.63 mg/L. Pipe fish was reported in northeast Florida 

region in the FMRI sampling, but in only one sampling event. For spot (Leiostomus xanthurus) 

the most commonly seen species in the northeast Florida region for which a SMAV is reported, 

the Guidance lists a SMAV of 0.70 mg/L, considerably lower that that of pipe fish. Following the 

approach used in toxics criteria development, the Guidance uses the mean LC5/LC50 ratio, 

here given as 1.38, to adjust upward the maximum tolerable acute value. Thus the CMC that is 

 44 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

considered as protective of most species is give as 2.3 mg/L, and this value has been used for 

the assessment of low dissolved oxygen effects in the LSJR estuary. 

Growth Effects 

To develop a measure of sub-lethal effects due to low dissolved oxygen, the Guidance relied 

upon previous studies that examined reductions in fish growth, usually during larval or juvenile 

life stages, due to low dissolved oxygen concentration. Growth is usually more sensitive than 

survival to low dissolved concentrations, though the Guidance notes several exceptions in which 

studies report greater rates of mortality than growth reduction. In general, invertebrates exhibit 

low acute dissolved oxygen concentrations, but a large range in growth reduction. Fish, on the 

other hand, exhibit higher acute concentrations but a relatively narrow range in growth 

reduction, and it is not unusual for fish species to exhibit considerable overlap in oxygen levels 

that cause mortality and growth reduction. Based upon a smaller number of studies that 

reported similar reductions in reproductive success at low dissolved oxygen levels, the 

Guidance concluded that oxygen levels that are protective of growth effects would also likely be 

protective of reproductive success. 

Of the 11 species for which growth effects data were found, 2 were collected in FMRI sampling: 

summer flounder (Paralichthys dentatus), a total of 9 individuals collected, and sheepshead 

minnow (Cyprinodon variegates), a total of 3 individuals collected. One of the most commonly 

caught fish in the FMRI sampling, silverside (Menidia spp.), at 10,342 individuals collected, is 

also listed in the Guidance growth effects data, though specifically for Menidia menidia, Atlantic 

silverside. The reported no observed effects levels (concentrations above which one would 

expect no reduction in growth) for summer flounder, sheepshead minnow, and Atlantic 

silverside are 4.39 – 7.23, 2.5 – 7.5, and 3.9, respectively. Based upon these ranges, it appears 

that the final chronic value (FCV) at which low dissolved oxygen is not expected to effect growth 

of 4.8 mg/L is appropriate for northeast Florida. 

Larval Recruitment 

To estimate the effects of hypoxic conditions at concentrations between 2.3 and 4.8 mg/L, the 

Guidance applies a larval recruitment model to estimate the number of individuals that are 

“recruited” from early life stages to juvenile stage. This model is based upon larval development 

time, larval season, attrition rate and patterns of vertical distribution. Nine genus had sufficient 

data to parameterize the model as developed in the Guidance. Two of these, Menidia and 

Scianops, are known to be present in northeast Florida based upon the FMRI sampling. The 

model develops recruitment curves based on the intensity and duration of low dissolved oxygen, 

and genus-specific curves for the two species found in northeast Florida developed the lowest 

and third lowest curves (Figure below from Guidance). 

The larval recruitment model can be adapted with regionally specific data. However, due to lack 

of specific data for northeast Florida species, and the possibility that species that have not been 

collected in the FMRI sampling program have been excluded due to human-induced changes in 

oxygen regime, the model formulation as provided in the Guidance has been used for the LSJR 

TMDL/PLRG process. 

 45 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Additional Considerations 

The methodology descried in the EPA estuarine dissolved oxygen guidance addresses only 

acute and chronic (growth) direct effects from low dissolved oxygen. Because of predator-prey 

interactions, the timing of reproductive activities, additional stressor effects under conditions of 

nutrient enrichment and eutrophication, direct effects may be mitigated or enhanced. Breitburg 

(2002), in her review of hypoxia effects on coastal fisheries, addresses many of the 

permutations of trophic alterations that may potentially occur. 

While the approach used is expected to be appropriate for other regions outside the Virginian 

Province estuaries, the Guidance does note that animals may have adapted to lower oxygen 

levels in regions of higher temperatures or with naturally high demands for dissolved oxygen. In 

particular, it may be appropriate at some point to develop regionally specific data for revising the 

larval recruitment model on which cumulative, sub-lethal effects are based. However, based 

upon the presence of species in northeast Florida that have been shown to exhibit reduced 

growth in the range of dissolved oxygen between 4 and 5 mg/L, and the possibility that certain 

species that are not shown to be present in this region from the FMRI sampling have been 

excluded due to human-induced reductions in dissolved oxygen, it is felt that the larval 

recruitment model represents a conservative estimate of potential harm that is less restrictive 

that the application of a strict 5 mg/L standard. 

Application of the Criteria 

The maximum acute value, growth effects threshold and larval recruitment model are combined 

into one relationship relating the intensity and duration of a given continuous, low dissolved 

oxygen event. This approach is graphically depicted in Figure 34. Above 4.8 mg/L, pelagic, 

estuarine organisms are assumed to suffer no chronic effect from hypoxia (defined as dissolved 

oxygen below saturation concentration; oxygen saturation concentration at 30 o C. and 15 ppt 

chlorinity = 6.5 mg/L). Oxygen levels below 2.3 mg/L are expected to have acute lethal effects 

to at least some organisms. Between these two values, the degree of mortality in the population 

is proportional to the duration of exposure, and the compilation of data from numerous doseresponse studies was used to develop the relationship seen in this figure. A given interval of 

low dissolved oxygen is considered to be a “dose” of potentially low dissolved oxygen, and is 

expressed as the fraction of the total duration of the interval at that concentration needed to 

cause mortality in at least 5 percent of the most sensitive species of the fish community. For 

example, the impairment index calculated duration of exposure to dissolved oxygen at 3 mg/L is 

5.57 days. A one day duration of 3 mg/L dissolved oxygen is considered to be 1/5.57 or 18 

percent of a lethal dose. Individual doses of continuous exposure that sum up to greater than 1 

are considered to be a lethal dose. 

Following the approach, 3 out of the 6 years of data collected at the Dames Point station 

exhibited one, long excursion of continuous low D.O., with durations from 4 to 7 weeks. 

Calculated impairment scores for Dames Point were 1.74, 3.57, and 1.07 for 1997,1999 and 

2001. In 1999, a large fish kill of many thousands of adult shad and menhaden occurred in this 

reach of the river, associated with this low D.O. event. No low D.O. events were measured at 

the Acosta Bridge station between 1996 and 2001 that qualify for chronic impairment under the 

EPA guidance approach, with the greatest score being 0.73, recorded in 1998. 

 46 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Dinoflagellate Bloom Potential 

The potential for nutrient and organic matter enrichment to stimulate the growth of marine 

dinoflagellate algal species represents one of the most significant detrimental effects attributable 

to estuarine eutrophication. Several toxic dinoflagellate species have been identified in regular 

plankton monitoring, including Karolina breve (red tide) and Prorocentrum minimum, and 

dinoflagellate infections have been postulated as a possible factor in ulcerative disease 

syndrome that plagued the LSJR during much of the early 1990’s. A monitoring program 

conducted in 19__ with the objective of determining the presence of Pfiesteria–like species 

discovered a previously unidentified dinoflagellate, subsequently named Cryptoperidineopsis 

brodii, to reside in LSJR mesohaline reach sediments. 

The tendency for dinoflagellate populations to increase in relative abundance under conditions 

of increasing potential diatom silica limitation leads to the possibility that high levels of nutrient 

enrichment, in excess of that balanced by bioavailable silica, may contribute disproportionately 

to dinoflagellate blooms. Dinoflagellate life cycles and survival strategies are extremely 

complex, however, and occurrence of high populations is poorly correlated with nutrient 

concentration or diatom biomass. For this reason, the limitation of dinoflagellate blooms exists 

as a qualitative target in LSJR TMDL development. In recent work investigating the relationship 

between nutrient enrichment effects on nuisance algal growth in the Indian River Lagoon, the 

occurrence of potentially toxic dinoflagellate blooms is identified as a significant water quality 

impairment (Phlips et al., 2003)). In this work, a level of 1,000,000 μm3

/ml algal biovolume 

(roughly equivalent 6 μg/L chlorophyll a) is suggested to define a marine bloom condition. 

 47 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

 48 

Florida Department of Environmental Protection 

Appendix D: Estimated Loads to the LSJR, 1995–99 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

 49 

Florida Department of Environmental Protection 

Table D1. Summary of Loads to the Lower St. Johns River, 1995. All values in metric tons per year.

Source or Source Category Total N Labile TON Refractory TON Total Inorganic N Total P Labile TNOP Refractory TNOP Total PO4 

O

 Buffalo Bluff Total 10765.1 4336.2 5373.0 1056.0 511.2 207.3 96.9 207.0  Natural Background 6659.7 1006.7 5432.5 220.5 290.8 97.9 97.3 95.6  Dunns Creek Total 1372.5 290.7 919.0 162.8 108.2 33.6 35.4 39.1  Natural Background 915.7 112.0 779.9 23.7 61.3 15.0 31.4 14.9 Upstream Total 12137.7 4627.0 6291.9 1218.8 619.3 240.9 132.3 246.1 Fresh Tidal NP Total 1068.4 371.7 505.6 191.1 211.2 54.9 22.7 133.6  Natural Nonpoint 626.3 203.8 387.9 34.6 56.8 11.1 6.7 38.9  Agriculture Contribution 384.1 126.1 124.7 133.4 136.9 35.4 13.4 88.1  Urban Contribution 53.2 39.3 -3.5 17.4 15.4 8.5 1.7 5.2  Other Nonpoint 4.7 2.5 -3.5 5.7 2.1 -0.1 0.9 1.3 Point Source 306.7 151.5 12.0 143.2 70.2 32.0 0.8 37.4 Oligohaline NP Total 1141.3 517.8 447.3 176.3 186.8 79.2 16.7 90.9  Natural Nonpoint 746.3 236.9 468.9 40.5 65.6 13.0 8.3 44.2  Agriculture Contribution 26.2 10.7 2.0 13.5 10.9 2.1 0.5 8.3  Urban Contribution 370.7 269.2 -10.1 111.6 110.0 64.0 7.8 38.2  Other Nonpoint -1.8 1.0 -13.5 10.7 0.5 0.0 0.2 0.3 Point Source 333.5 49.6 3.9 279.9 72.1 11.2 0.3 60.6 Meso-Polyhaline NP Total 440.2 223.2 120.6 96.4 92.0 44.0 6.6 41.4  Natural Nonpoint 218.4 68.0 138.5 11.9 19.8 3.8 2.5 13.6  Agriculture Contribution 13.4 5.3 1.1 7.0 5.3 1.2 0.2 4.0  Urban Contribution 209.9 151.9 -10.7 68.8 66.6 39.2 3.8 23.6  Other Nonpoint -1.5 -2.1 -8.2 8.8 0.2 -0.2 0.2 0.2 Point Source 1147.4 238.9 18.9 889.6 294.4 46.9 1.2 246.2 Total Atmospheric Dep. 243.0 5.0LSJRB Summary Total Natural Nonpoint 1591.0 508.7 995.3 86.9 142.2 28.0 17.5 96.7  Total Augmented Nonpoint 1059.0 603.9 78.2 376.8 347.9 150.2 28.6 169.1  Total Point Source 1787.6 440.0 34.9 1312.7 436.6 90.2 2.3 344.2 Grand Total 16818.3 6179.6 7400.4 2995.2 1551.0 509.2 180.6 856.1 2Notes: N= Nitrogen; P=Phosphorus; C=Carbon. NP=Nonpoint Sources. LSJRB Summary sums loads for only the LSJRB downstream of Dunns Creek. 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

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Florida Department of Environmental Protection 

Table D2. Summary of Loads to the Lower St. Johns River, 1996. All values in metric tons per year. 

Source or Source Category Total N Labile TON Refractory TON Total Inorganic N Total P Labile TNOP Refractory TNOP Total PO4 

O

 Buffalo Bluff Total 8609.9 4828.1 3252.4 529.4 385.0 241.4 48.1 95.3  Natural Background 4451.6 1100.3 3252.4 98.9 221.1 122.7 48.1 50.4  Dunns Creek Total 898.0 172.5 595.7 129.8 42.5 11.8 13.7 17.1  Natural Background 716.0 85.8 595.7 34.5 34.1 9.6 13.7 10.9 Upstream Total 9507.9 5000.6 3848.1 659.2 427.5 253.2 61.7 112.5 Fresh Tidal NP Total 578.6 187.5 289.3 101.8 93.6 25.7 11.5 56.4  Natural Nonpoint 365.6 105.5 243.7 16.5 32.0 6.0 4.5 21.5  Agriculture Contribution 177.0 56.0 49.7 71.3 51.8 15.0 5.6 31.2  Urban Contribution 30.8 25.7 -5.1 10.2 8.6 4.7 0.9 2.9  Other Nonpoint 5.2 0.3 1.0 3.9 1.3 0.0 0.6 0.7 Point Source 285.6 144.6 11.5 129.6 66.0 30.5 0.8 34.7 Oligohaline NP Total 676.8 300.0 264.0 112.8 113.7 47.0 10.1 56.6  Natural Nonpoint 427.3 124.3 281.9 21.0 38.3 7.1 5.2 26.1  Agriculture Contribution 18.0 7.2 1.8 9.0 6.6 1.2 0.2 5.1  Urban Contribution 230.5 51.4 -13.5 77.0 68.0 38.6 4.5 24.9  Other Nonpoint 1.0 117.0 -6.2 5.8 0.8 0.1 0.2 0.4 Point Source 322.5 42.3 3.4 276.8 65.6 10.5 0.3 54.9 Meso-Polyhaline NP Total 422.7 210.3 119.2 93.2 87.2 39.6 6.3 41.3  Natural Nonpoint 211.3 62.5 137.7 11.0 19.6 3.5 2.5 13.5  Agriculture Contribution 17.8 6.6 1.8 9.4 7.5 1.6 0.3 5.6  Urban Contribution 193.3 141.7 -14.2 65.8 59.4 34.5 3.3 21.6  Other Nonpoint 0.4 -0.6 -6.2 7.1 0.8 -0.1 0.3 0.6 Point Source 1144.4 251.6 20.0 872.9 328.9 50.8 1.3 276.9 Total Atmospheric Dep. 243.0 5.0LSJRB Summary Total Natural Nonpoint 1004.2 292.3 663.4 48.5 89.8 16.6 12.1 61.2  Total Augmented Nonpoint 673.9 405.5 9.1 259.3 204.6 95.7 15.8 93.1  Total Point Source 1752.5 438.5 34.8 1279.3 460.5 91.7 2.3 366.5 Grand Total 13181.5 6136.9 4555.3 2246.3 1187.5 457.1 91.9 633.2 
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Table D3. Summary of Loads to the Lower St. Johns River, 1997. All values in metric tons per year. 

Source or Source Category Total N Labile TON Refractory TON Total Inorganic N Total P Labile TNOP Refractory TNOP Total PO4 

O

 Buffalo Bluff Total 4849.3 3606.6 1061.3 181.4 173.2 148.6 12.9 11.6  Natural Background 1880.2 792.5 1061.3 26.4 117.5 85.7 12.9 18.8  Dunns Creek Total 933.4 318.0 564.3 51.2 59.9 27.1 15.6 17.2  Natural Background 711.2 133.1 564.3 13.8 35.8 15.2 15.6 4.9 Upstream Total 5782.7 3924.6 1625.5 232.6 233.1 175.7 28.6 28.8 Fresh Tidal NP Total 992.8 341.2 430.4 221.2 158.4 54.4 20.6 83.4  Natural Nonpoint 532.7 181.2 321.9 29.6 44.8 9.7 5.5 29.5  Agriculture Contribution 405.3 122.0 109.6 173.7 97.5 35.5 12.1 49.9  Urban Contribution 49.1 39.2 -1.0 10.9 14.4 9.0 2.0 3.4  Other Nonpoint 5.7 -1.2 0.0 7.0 1.7 0.1 1.0 0.5 Point Source 299.6 86.6 73.1 139.7 69.1 24.0 7.0 38.1 Oligohaline NP Total 728.4 325.9 302.4 100.1 110.4 46.5 10.8 53.0  Natural Nonpoint 501.7 163.3 310.9 27.4 42.8 8.9 5.4 28.4  Agriculture Contribution 16.4 6.8 1.3 8.4 6.9 1.3 0.3 5.3  Urban Contribution 211.9 156.1 -1.4 57.3 60.6 36.3 5.0 19.3  Other Nonpoint -1.6 -0.3 -8.3 7.0 0.1 0.0 0.1 0.0 Point Source 341.3 45.9 9.8 285.6 73.6 11.5 0.7 61.5 Meso-Polyhaline NP Total 342.7 182.4 88.7 71.6 69.6 35.1 4.7 29.8  Natural Nonpoint 162.7 52.0 101.9 8.8 13.9 2.9 1.8 9.2  Agriculture Contribution 9.9 4.0 0.4 5.5 3.5 0.6 0.0 2.9  Urban Contribution 170.9 128.3 -8.5 51.1 52.0 31.6 2.7 17.7  Other Nonpoint -0.8 -1.9 -5.0 6.1 0.2 0.1 0.2 -0.1 Point Source 1187.7 251.1 33.7 902.9 334.6 71.4 3.1 260.1 Total Atmospheric Dep. 243.0 5.0LSJRB Summary Total Natural Nonpoint 1197.1 396.5 734.6 65.9 101.4 21.5 12.7 67.2  Total Augmented Nonpoint 867.0 453.0 87.0 327.0 236.9 114.6 23.3 99.0  Total Point Source 1828.6 383.6 116.6 1328.2 477.4 106.9 10.8 359.7 Grand Total 9918.4 5157.8 2563.7 1953.6 1053.8 418.7 75.4 554.7 
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Florida Department of Environmental Protection 

Table D4. Summary of Loads to the Lower St. Johns River, 1998. All values in metric tons per year. 

Source or Source Category Total N Labile TON Refractory TON Total Inorganic N Total P Labile TNOP Refractory TNOP Total PO4 

O

 Buffalo Bluff Total 8561.5 4942.4 3175.9 443.1 341.8 201.8 42.5 97.4  Natural Background 4428.1 1189.7 3175.9 62.5 246.4 140.0 42.5 63.9  Dunns Creek Total 971.2 217.6 681.9 71.7 51.3 15.8 15.9 19.7  Natural Background 813.6 108.2 681.9 23.5 39.4 11.1 15.9 12.4 Upstream Total 9532.7 5160.0 3857.8 514.9 393.1 217.6 58.4 117.1 Fresh Tidal NP Total 1652.2 480.2 935.0 237.0 222.9 53.8 31.1 138.0  Natural Nonpoint 1188.3 284.7 864.2 39.4 103.4 17.3 16.7 69.4  Agriculture Contribution 350.3 111.7 93.9 144.7 92.2 27.3 11.9 53.0  Urban Contribution 110.4 92.5 -21.4 39.4 25.8 13.4 2.8 9.6  Other Nonpoint 3.1 -8.7 -1.7 13.6 1.5 -4.2 -0.2 5.9 Point Source 274.2 82.4 57.1 134.5 62.1 21.9 5.1 35.0 Oligohaline NP Total 1236.9 492.7 565.8 178.4 171.8 63.8 18.4 89.6  Natural Nonpoint 830.1 199.7 601.6 28.8 72.4 12.1 11.6 48.7  Agriculture Contribution 35.9 17.9 9.5 8.5 8.7 5.9 2.4 0.5  Urban Contribution 374.4 282.0 -33.2 125.6 90.6 50.4 6.3 33.9  Other Nonpoint -3.5 -6.9 -12.1 15.4 0.1 -4.5 -1.9 6.5 Point Source 301.3 53.7 9.6 238.0 81.4 13.2 0.7 67.5 Meso-Polyhaline NP Total 867.0 436.2 254.1 176.7 152.0 68.5 11.4 72.1  Natural Nonpoint 426.5 109.6 299.9 17.0 37.7 6.5 5.7 25.5  Agriculture Contribution 38.3 7.3 -1.5 32.5 11.8 -3.1 -1.1 16.1  Urban Contribution 404.1 315.7 -40.2 128.6 101.5 59.8 4.8 36.9  Other Nonpoint -1.8 3.6 -4.1 -1.3 0.9 5.3 2.0 -6.3 Point Source 1267.0 279.4 38.3 949.3 341.5 70.7 3.3 267.6 Total Atmospheric Dep. 243.0 5.0LSJRB Summary Total Natural Nonpoint 2444.9 594.0 1765.7 85.2 213.5 35.8 34.0 143.6  Total Augmented Nonpoint 1311.2 815.2 -10.8 506.8 333.2 150.3 26.8 156.1  Total Point Source 1842.4 415.5 105.1 1321.8 485.0 105.8 9.1 370.1 Grand Total 15374.2 6984.7 5717.8 2428.7 1429.8 509.5 128.4 786.9 2
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Florida Department of Environmental Protection 

Table D5. Summary of Loads to the Lower St. Johns River, 1999. All values in metric tons per year. 

Source or Source Category Total N Labile TON Refractory TON Total Inorganic N Total P Labile TNOP Refractory TNOP Total PO4 

O

 Buffalo Bluff Total 5280.2 3876.3 1268.0 182.0 183.4 150.2 17.2 17.9  Natural Background 2091.0 815.0 1250.3 25.7 121.3 83.3 16.9 21.1  Dunns Creek Total -166.6 -120.9 -45.0 -0.8 -8.9 -6.5 -1.9 -0.6  Natural Background -80.4 -35.3 -45.2 0.2 -3.9 -2.0 -1.9 0.0 Upstream Total 5113.6 3755.4 1223.0 181.2 174.5 143.7 15.3 17.4 Fresh Tidal NP Total 248.7 84.8 119.4 44.5 54.5 13.4 5.6 35.5  Natural Nonpoint 139.6 39.3 93.9 6.5 13.2 2.3 1.7 9.2  Agriculture Contribution 103.1 35.0 35.1 33.0 38.9 9.6 3.7 25.6  Urban Contribution 9.3 7.6 -1.4 3.2 2.6 1.5 0.2 0.9  Other Nonpoint -3.3 3.0 -8.1 1.8 -0.2 0.0 0.0 -0.3 Point Source 275.3 144.0 11.4 119.8 64.5 30.3 0.8 33.4 Oligohaline NP Total 236.9 103.3 93.4 40.2 40.8 16.0 3.6 21.2  Natural Nonpoint 162.4 45.3 109.1 7.9 15.6 2.6 2.0 10.9  Agriculture Contribution 5.9 2.3 0.5 3.1 2.6 0.5 0.1 2.0  Urban Contribution 74.9 51.9 -3.5 26.5 23.4 12.8 1.7 9.0  Other Nonpoint -6.3 3.8 -12.7 2.6 -0.8 0.1 -0.2 -0.7 Point Source 305.2 46.3 3.7 255.2 81.9 13.1 0.3 68.5 Meso-Polyhaline NP Total 156.5 76.9 44.0 35.7 33.1 14.9 2.4 15.9  Natural Nonpoint 79.9 21.9 54.1 3.9 7.6 1.3 1.0 5.4  Agriculture Contribution 6.9 2.6 0.8 3.6 2.8 0.6 0.1 2.0  Urban Contribution 71.4 51.6 -5.6 25.5 22.8 13.0 1.2 8.5  Other Nonpoint -1.8 0.8 -5.3 2.7 0.0 0.0 0.0 0.0 Point Source 1121.5 206.0 16.3 899.2 330.3 50.0 1.2 279.1 Total Atmospheric Dep. 243.0 5.0LSJRB Summary Total Natural Nonpoint 381.9 106.5 257.1 18.3 36.4 6.2 4.8 25.5  Total Augmented Nonpoint 260.2 158.5 -0.3 102.0 92.0 38.1 6.8 47.0  Total Point Source 1702.0 396.4 31.4 1274.2 476.7 93.4 2.3 381.0 Grand Total 7700.7 4416.8 1511.2 1575.7 784.6 281.4 29.2 470.9 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix E: Description of State and Federal 

Stormwater Programs 

In 1982, Florida became the first state in the country to implement statewide regulations to 

address the issue of nonpoint source pollution by requiring new development and 

redevelopment to treat stormwater before it is discharged. The Stormwater Rule, as authorized 

in Chapter 403, F.S., was established as a technology-based program that relies on the 

implementation of BMPs that are designed to achieve a specific level of treatment (i.e., 

performance standards) as set forth in Rule 62-40, F.A.C. In 1994, the Department’s 

stormwater treatment requirements were integrated with the stormwater flood control 

requirements of the state’s water management districts, along with wetland protection 

requirements, into the Environmental Resource Permit regulations 

Rule 62-40, F.A.C., also requires the water management districts to establish stormwater 

PLRGs and adopt them as part of a Surface Water Improvement and Management (SWIM) 

plan, other watershed plan, or rule. Stormwater PLRGs are a major component of the load 

allocation part of a TMDL. 

In 1987, the U.S. Congress established Section 402(p) as part of the federal Clean Water Act 

Reauthorization. This section of the law amended the scope of the federal NPDES Stormwater 

Permitting Program to designate certain stormwater discharges as “point sources” of pollution. 

The EPA promulgated regulations and began implementing the Phase I NPDES Stormwater 

Program in 1990. These stormwater discharges include certain discharges that are associated 

with industrial activities designated by specific standard industrial classification (SIC) codes, 

construction sites disturbing 5 or more acres of land, and master drainage systems of local 

governments with a population above 100,000, which are better known as MS4s. However, 

because the master drainage systems of most local governments in Florida are interconnected, 

the EPA has implemented Phase 1 of the MS4 permitting program on a countywide basis, which 

brings in all cities (incorporated areas), Chapter 298 urban water control districts, and FDOT 

throughout the 15 counties meeting the population criteria. The EPA authorized the Department 

to implement the NPDES Stormwater Program (with the exception of Indian lands) in October 

2000. 

An important difference between the federal and the state’s stormwater/environmental resource 

permitting programs is that the NPDES Program covers both new and existing discharges, while 

the state’s program focuses on new discharges only. Additionally, Phase II of the NPDES 

Program, implemented in 2003, expands the need for these permits to construction sites 

between 1 and 5 acres, and to local governments with as few as 10,000 people. These revised 

rules require that these additional activities obtain permits by 2003. While these urban 

stormwater discharges are now technically referred to as “point sources” for the purpose of 

regulation, they are still diffuse sources of pollution that cannot be easily collected and treated 

by a central treatment facility, as are other point sources of pollution, such as domestic and 

industrial wastewater discharges. It should be noted that all MS4 permits issued in Florida 

include a reopener clause that allows permit revisions to implement TMDLs when the 

implementation plan is formally adopted. 

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FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix F: Examples of DO Calibration Figures for 

the Water Quality Model 

 55 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Acosta Bridge

Daily-Averaged D. O. (mg L-1)

Observed

Simulated

r2 = 0.79

rms = 0.52

AVRE = 7.6%

Figure F1. Accuracy of Model DO Predictions for Acosta Bridge 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Dames Point

Daily-Averaged D. O. (mg L-1)

r2 = 0.74

rms = 0.58

AVRE = 10.5%

Observed

Simulated

Figure F2. Accuracy of Model DO Predictions for Dames Point 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix G: Examples of Chlorophyll a Calibration 

Figures for the Water Quality Model 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure G1. Comparisons of Model Predictions Versus Measured Values for 

Chlorophyll a at Racy Point 

Figure G2. Comparisons of Model Predictions Versus Measured Values for 

Chlorophyll a at Watson Island 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure G3. Accuracy of Model Predictions of Average Annual Chlorophyll a for the 

Freshwater Section 

Average Annual Chlorophyll Freshwater Section

Observed Average Chlorophyll

Simulated Average Chlorophyll

r2 = 0.81

rms error = 3.9

slope = 0.67

intercept = 6.2

Figure G4. Accuracy of Model Predictions for Chlorophyll a Percent Exceedances for 

the Freshwater Section 

Percent Exceedence of 40 μgL-1 Chlorophyll Freshwater Section

Observed % Exceedence of 40 μgL-1 Chlorophyll

Simulated % Exceedence of 40 

μgL-1 Chlorophyll

r2 = 0.75

rms error = 5.1

slope = 0.76

intercept = 3.5

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FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix H: Responsiveness Summary to Public 

Comments on Draft TMDL of 2003 

EPA Comments on the Department’s Nutrients TMDL for the 

Lower St. Johns River, August 28, 2003 

1. In order for EPA to accept the water quality target, the concepts in the following 

paragraph should be addressed in the TMDL development discussion in section 1.2: 

 The Department recognizes that it may be appropriate to revise the TMDL in the future 

when more information has been collected and analyzed. With such possible 

revisions in mind, this TMDL is characterized as an adaptive management TMDL. In 

an adaptive management TMDL, the Department used the best available information 

at the time to establish an interpretation of their narrative nutrient standard to derive 

the water quality end point as the basis for the TMDL. However, the adaptive 

management approach recognizes that additional data and information may be 

necessary to validate assumptions of the TMDL, specifically the interpretation of the 

nutrient narrative criterion as 40 μg/L chlorophyll a not to be exceeded more than 10 

percent of the time, and to provide greater certainty that the TMDL will achieve use 

support of the St. Johns River and prevent an imbalance in natural populations of 

aquatic flora and fauna. 

Response: The Department added similar text to Section 7. 

2. The background information in section 1.3 should include hydrologic and geologic 

information about the Lower St. Johns River since nonpoint sources contribute 

significantly to the nutrient impairment. A good source of information is FDEP’s 

“Basin Status Report: Lower St. Johns” dated June 2002. 

Response: A sentence was added to Section 1.3 referencing the Basin Status Report. 

3. The problem statement in section 2 should describe the declining water quality in the 

Lower St. Johns River. Good information is included in the Basin Status Report 

mentioned above (see p. 53 & 54). 

Response: A sentence was added to Section 1.3 referencing the Basin Status Report. 

4. The problem statement in section 2 should include a summary of the water quality 

data used to verify segments of the river as impaired. The data should be compared 

to water quality criteria noting the frequency and extent of any violations. 

Response: A table was added to the document (Appendix I) summarizing the annual 

average chlorophyll a values and TSIs for the segments of the main stem that were verified 

as impaired. 

5. Please inform EPA about the status of adopting the LSJR verified list by Secretarial 

Order since it is a prerequisite for adopting this TMDL. 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Response: Text in Sections 1.1 and 2.1 was revised to note that the Verified List for the 

main stem of the LSJR was adopted by Secretarial Order on September 4, 2003. 

6. The last paragraph in section 3.2 needs to be deleted. The concepts in the following 

paragraph should be discussed in the TMDL report: 

The current nutrient TMDL for the estuarine portion of the St. Johns River is based on 

maintaining DO levels above those that have been calculated using the EPA method 

in the document Ambient Aquatic Life Water Quality Criteria for Dissolved Oxygen 

(Saltwater): Cape Cod to Cape Hatteras (EPA-822-R-00-012, November 2000). This 

method does not implement the Florida water quality standards that are currently in 

place for the river at this location. Since this new approach is being used, the 

SJRWMD and FDEP are pursuing development of a SSAC for DO for this portion of 

the river in accordance with 62-302.500(2)(f) F.A.C. Since the segments in this portion 

of the river meet water quality standards for DO and this TMDL proposes nutrient 

reductions to address a nutrient impairment, it will only have beneficial impacts on 

DO. Therefore, even though FDEP is not using the approved water quality standard 

as a target for this TMDL, implementation will not result in degradation with respect to 

DO. In addition, the SJRWMD will continue work related to nutrient loads and algal 

response for this section of the river. Algal response to increased nutrient loads 

would be more appropriate to use when evaluating the narrative nutrient criterion, 

which has balanced, natural populations of aquatic flora and fauna as its endpoint. 

Response: The last paragraph in Section 3.2 of the draft document was deleted, and the 

requested text was added to the section (with the exception of the last two sentences). 

7. In order for EPA to accept the water quality target, the concepts in the following 

paragraph should be discussed in section 3.3: 

Studies have shown that when chlorophyll a levels rise above 40 μg/L , a shift in algal 

types occurs: blue-green algae begin to dominate the system, toxic algal species 

begin to increase, and zooplankton communities begin to decline. While maintaining 

chlorophyll a levels below 40 μg/L 90 percent of the time may prevent an imbalance in 

natural populations of aquatic flora and fauna under average conditions, it is 

uncertain whether these levels will be fully protective in this portion of the river under 

critical flow conditions, in a prolonged low flow situation, or during the extended 

growing season with less than average flows. For this reason, continued study of the 

river system is necessary to determine if a seasonal average maximum or yearly 

average maximum level of chlorophyll a should be established to protect against 

imbalances in natural populations of aquatic flora and fauna due to high nutrient 

levels. Specifically, a series of studies is needed to demonstrate: (1) that progress is 

being made towards reducing nutrient loads by the required 30 percent or that 

progress towards reaching the percent reduction goal is being made, (2) that once the 

30 percent reduction goal is reached, it has resulted in chlorophyll a levels that do not 

exceed 40 μg/L more than 10 percent of the time, and (3) that once the chlorophyll a 

target is reached, it has resulted in achievement of the narrative nutrient criterion (i.e., 

balanced, natural populations of aquatic flora and fauna). 

Response: The Department added similar text to Section 3.3. 

8. According to the nutrient criterion discussion in section 3.3, “the water quality target 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

is being implemented as a long-term average value rather than a worst case year...” 

However, it appears from the discussion in section 5.5 that the model was applied on 

an annual basis. Since the target is based on not exceeding a chlorophyll a value of 

40 μg/L for more than 40 consecutive days (which would primarily apply over the 

summer months/growing season), EPA cannot support the target if it is applied for 

more than an annual duration. FDEP must apply the target on an annual basis in 

order for EPA to accept it as a reasonable interpretation of the narrative nutrient 

criterion. 

Response: Based on subsequent discussions with EPA Region 4 staff, it was agreed that 

the application of the chlorophyll a target on a long-term average basis was appropriate as 

long as the Department added the text requested in Comments 1 and 7, and provided 

additional explanation (as follows) about how application of the target as a long-term 

average basis is adequately protective. 

The TMDL stakeholders, TMDL Executive Committee, SJRWMD, and Department all 

agreed that it would be overly conservative to apply the threshold in a worst-case year and 

that a long-term average was adequately protective of the river. There were many reasons 

for this position, including the fact that there are already conservative elements of the 

modeling (applied in the worst-case WBID, for example), it is common practice for nutrient 

TMDLs to be based on “design runs” that estimate long-term average conditions, stormwater 

treatment design criteria and BMPs (implementation of which will be how most of the 

nonpoint source reductions will be achieved) are typically designed for rain events that 

would not be typical of the worst case year, and external load model estimates of nonpoint 

source loading would overestimate loading for dry years because they would not adequately 

take into account the increased removal provided by stormwater treatment facilities. 

Nutrient management activities for nonpoint sources will naturally be more effective at dry 

conditions such that additional nonpoint source reductions required for a worst-case dry 

year are not needed and would result in the overdesign of stormwater facilities. 

It should be noted that the target is for the chlorophyll a to be less than 40 μg/L less than 10 

percent of the time, rather than less than 40 days as stated in the EPA’s comment. 

9. A land use map and a tabular breakdown of the land use categories in the basin would 

be a helpful accompaniment to the source information contained in section 4. 

Response: The document by Hendrickson et al. (2002), which describes the external load 

assessment and which is referenced in Section 4.1, provides detailed information about land 

uses. Further, the key output of the external load assessment (the estimated loads from 

each major land use) were provided in Appendix D of this document. 

10. Please provide EPA with a copy of the document described in section 4.1 as 

containing a report on the computations involved in developing the external load for 

the Lower St. Johns River. 

Response: A final copy of the document will be provided with the TMDL when it is 

submitted to the EPA. 

11. According to section 4.2, “[t]here are 36 permitted wastewater treatment facilities 

that discharge nutrient loads directly into the LSJR (Table 2), with a total of 32 

domestic wastewater facilities and 4 industrial wastewater facilities.” However, the 

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previously mentioned Basin Status Report states the following: 

“The basin contains 184 point sources, which are permitted to discharge to surface 

waters or land application systems, or both...One hundred and thirty-seven of these 

are domestic wastewater treatment facilities (the largest component of point 

sources), 45 are industrial waste facilities, 2 are concrete batch plants, and 1 is a 

residual/septage management facility...One hundred and nine point sources are 

permitted to discharge to surface waters under the National Pollutant Discharge 

Elimination System (NPDES)...” 

Please explain the discrepancy in the reported numbers of permitted facilities in the 

basin. Are the additional point sources discharging to waters that do not directly 

impact the TMDL segments? 

Response: Yes, the additional point sources listed in the Basin Status Report do not 

directly discharge to the LSJR. Their loadings are indirectly assessed as part of the load 

from tributaries to the basin. 

12. The non-point source discussion in section 4.3 needs to identify what non-point 

sources exist in the basin. According to the previously mentioned Basin Status 

Report, non-point sources of nutrient loading to the Lower St. Johns River basin 

include onsite sewage treatment and disposal systems (OSTDSs), tributaries (e.g., 

Black Creek, Dunns Creek, Deep Creek, Rice Creek, Julington Creek, Trout Creek, 

Sixmile Creek, Governors Creek, Clarkes Creek, Cedar Creek, Camp Branch, Mill 

Branch, Dog Branch, etc.), stormwater runoff, marinas, silviculture, row crop 

agriculture (notably the Tri-County Agricultural Area), dairies, and urban 

development. 

Response: As noted in the response to Comments 9 and 10, the referenced document by 

Hendrickson et al. (2002) provides a detailed assessment of the pollutant loadings to the 

river, including the major tributaries. Predicted loadings from this report were then provided 

in Appendix D of the TMDL document. 

 

13. The atmospheric deposition discussion in section 4.3.2 only mentions nitrogen 

loading. Please explain why phosphorus loading by atmospheric deposition was not 

considered. 

Response: Text was added to Section 4.4.2 noting that atmospheric deposition of 

phosphorus was not included in the modeling and TMDL assessment because it is 

expected to be a very minor source of phosphorus to the basin. 

14. The method that was used to identifying sources in the LSJR basin should be 

identified in the TMDL. For example, the Watershed Characterization System (WCS) 

was used to characterize sources for the Hatchet Creek total coliforms TMDL. 

Response: As noted in the response to Comments 9 and 10, the referenced document by 

Hendrickson et al. (2002) provides a detailed assessment of the pollutant loadings to the 

river, including a description of the methods used to identify sources. 

15. The source assessment discussion should also include information about applicable 

stormwater rules. Please consider incorporating the language in Attachments A and 

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B. 

Response: Text on the state’s stormwater rules and NPDES Stormwater Program have 

been added as Appendix A. 

16. Please explain why the point sources discharging directly to the St. Johns River were 

evaluated based on their 1997-98 discharge flows and loads rather than a more 

current time period. 

Response: It is important to note that the referenced point source loads were the loads 

used as the starting point for the allocation process, which is designed to equitably assign 

reductions to both point sources and nonpoint sources (percent reductions were calculated 

against these starting points rather than current loading or design loads). The Allocation 

Technical Advisory Committee Report actually recommends that the Department use the 

permitted load (if available) as the starting point, but it was determined that in many cases 

the permitted load was significantly higher than current loading. Based on discussions at 

Stakeholders Committee and TMDL Executive Committee meetings, stakeholders 

recommended that we use the 1997–98 loadings with an allowance for anticipated growth 

over the next few years as the starting point for load reductions. 

17. According to section 5.5, nitrogen was determined to be the key nutrient that needed 

to be reduced to meet the target. How was this determination made? 

Response: As described in the TMDL document, nitrogen is the key limiting nutrient in the 

oligohaline/mesohaline portion of the river, while both nitrogen and phosphorus are 

colimiting in the freshwater portion of the river. Nitrogen alone is the limiting nutrient in the 

saline portions of the river because the dominant nitrogen-fixing algae in the river are 

freshwater species and die out as they move downstream. 

18. Based on the attached maps of the Jacksonville MS4 area, small municipalities in the 

freshwater section of the river (including Fruit Cove and Green Cove Springs) are 

covered by Phase II of the NPDES stormwater program. The wasteload allocation 

discussion in section 6.3 needs to be revised accordingly. 

Response: The wasteload allocation in Section 6.3 was revised to include an allocation 

(expressed as a percent reduction) to NPDES stormwater discharges. 

19. The following statement in section 6.4 does not appear to provide a margin of safety 

for preventing imbalance: “In the freshwater zone, multiple years of phytoplankton 

and zooplankton field measurements were evaluated to establish the site-specific 

chlorophyll a level beyond which zooplankton abundance and diversity started to 

decline.” Rather, this statement appears to provide a margin of safety for preventing 

toxicity. 

Response: The quoted text merely provides background information relevant to 

determination of the chlorophyll a target. The key concept related to providing a margin of 

safety in the paragraph was the fact that the long-term conditions used were slightly drier 

than normal. 

20. The following statement in section 6.4 is not a valid margin of safety because TMDLs 

should never assume that permit limits are protective: “Finally, point source flows 

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and loads used in the WLA for the freshwater zone were based upon existing flows 

and loads with an allowance for growth rather than assuming permitted limits.” 

Waste load allocations should only be calculated considering in-stream water quality 

effects, not current permit limits. 

Response: Again, the quoted text was meant to provide background information relevant to 

how the point source loads were established. The key text, which we strongly agree with, 

was that an implicit margin of safety is provided by this approach because it is extremely 

unlikely that all point sources would simultaneously discharge at their full WLA. 

21. Use of the DO minimum threshold from the 1999 EPA document does not quality (sic) 

as a margin of safety because no site-specific evidence has been provided that the 

threshold is applicable in the Lower St. Johns River. Moreover, it is not an approved 

water quality criterion. 

Response: We are confident that applying this methodology to Florida is conservative 

because Florida species are acclimated to lower DO values given the warmer temperatures 

in Florida, which result in lower DO saturation levels. 

22. The seasonal variability section is mis-numbered. It should be section 6.5. 

Response: The section was renumbered. 

Comments by Michael Hartman (as Private Citizen), August 1, 

2003 

Mr. Hartman provided comments on several aspects of the TMDL, including the TMDL 

development process and the technical basis of the TMDL. Comments on the process 

included: (1) comments about the role of the facilitator hired by FDEP and SJRWMD to 

coordinate with stakeholders and facilitate stakeholder and Executive Committee 

meetings, (2) a request to attract broader public participation in the process, (3) a 

suggestion to include academia in the process, and (4) a comment noting how the 

organizational structure took a long time to evolve. Technical comments included: (1) a 

comment that the TMDL should make reference to a strong commitment to conducting 

bioassessments to determine effectiveness of TMDL implementation, with local 

universities playing some role in the bioassessments, (2) a comment that all wastewater 

facilities should be required to reduce TN and TP by at least 50 percent based on fairness 

issues, (3) a request for a bigger margin of safety, (4) a comment that using long-term 

average conditions is not a conservative approach and that a statistical approach should 

be used to determine the lower 90 percent confidence interval around the mean river flow 

over a 10-20 year period, and (5) comments about the alternative DO threshold used in 

the estuarine portion of the river (that our ecology is vastly different than in the more 

northern coastal estuaries and that DO levels in the river and area tributaries are likely 

below the DO criterion. 

Response: The comments on the TMDL development process will be considered by the 

Department as we continue with development of the BMAP for the TMDL and as we move to 

other basins. While we did not make any changes to the document in response to Mr. 

Hartman’s technical comments, our general responses are as follows: (1) we plan to develop a 

monitoring plan as part of the B-MAP and this monitoring will assess how the river responds to 

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reductions in nutrient loading, (2) the ultimate reductions for each wastewater facility will be 

determined as part of the stakeholder driven B-MAP development process, (3) we believe the 

implicit margin of safety is adequate, (4) we believe that the application of the nutrient targets 

using long-term average conditions is appropriate, and (5) we acknowledge that conditions in 

the LSJR are different than Cape Cod to Cape Hatteras, but that the warmer temperatures in 

Florida actually add an implicit margin of safety because Florida species are likely acclimated to 

lower DO levels. 

Comments from Ray Avery, Executive Director, Clay County 

Utility Authority, August 8, 2003 

Mr. Avery provided several comments about the draft allocation table, and requested that 

the Department determine a uniform TN concentration for all facilities to achieve the 

necessary load reductions. He noted Clay County voluntarily reduced its TN 

concentrations to an average of 3.5 mg/L and that the current allocation approach may 

penalize facilities that proactively reduce loadings because it did not allow any room to 

increase their flow. 

Response: Department staff from the Northeast District met with Mr. Avery and subsequently 

revised the allocation spreadsheet provided in the TMDL document upon discussion with Clay 

County and other dischargers. It should be noted however, that the actual allocations will be 

developed as part of the BMAP process. 

Comments from Bill Bartnick, Environmental Administrator, 

Florida Department of Agriculture and Consumer Services, 

August 26, 2003 

Mr. Bartnick expressed concern about a statement in the draft document that “the 

nutrient TMDL also needed to address the impact of nutrients on DO levels” and 

commented about the importance of color on DO in the freshwater portion of the river 

(noting that the river acts more like a “tannic lake” than a true riverine system). He also 

requested that the Department use more updated land use information for dairies and 

potato farming in the oligohaline/mesohaline reach of the river, and commented about 

the allocation process for agricultural operations. 

Response: We agree that color and organic load have an important impact on river DO values, 

but stand by the original comment that the TMDL should also address the impact of nutrients on 

DO levels. As for the comments about land use information and the allocation process, we plan 

to use the updated land use information during the B-MAP development process to refine the 

allocations, which will take into account participation rates of area farmers. 

Comments from Donna Kaluzniak, Public Utilities Director, 

Atlantic Beach, August 26, 2003 

Ms. Kaluzniak provided comments on several aspects of the TMDL, including expressing 

concern about the accuracy of loading values used for wastewater facilities at the mouth 

of the river, asking about the source of metals in domestic wastewater discharges, 

asking several questions about nutrient loading from the city of Atlantic Beach’s 

wastewater treatment plants and about potential treatment and disposal alternatives, 

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expressing the opinion that the document contradicts itself regarding DO levels, 

commenting about verification of the model, and asking about the sources of loading to 

the river. 

Response: We are confident that the loads used for the wastewater facilities are as accurate as 

possible. Regarding the question about metals in the effluent, we are not sure of the relevance 

of the question to this particular TMDL and assume the comment was in response to the list of 

verified impaired segments in the main stem of the river (Table 1), which included several metal 

listings. As for the questions about the city of Atlantic Beach WTP, these issues will be 

addressed during the development of the B-MAP for the TMDL. It is not clear what Ms. 

Kaluzniak found contradictory about DO levels. And finally, comments regarding the verification 

of the model and the pollutant source load estimates should be well addressed by the 

referenced documents by the SJRWMD. 

Comments from Captain L. S. Cotton, Naval Air Station, 

Jacksonville, August 28, 2003 

Captain Cotton expressed concern about the starting point used for wastewater facilities, 

noting that not using the permitted load severely impacts military operational flexibility 

because they are not operating at full capacity. He also asked about the method for 

projecting future growth, why the commitment by Jacksonville Electric Authority (JEA) to 

reduce nitrogen loadings by 50 percent was not taken into account, and why the 

allocation spreadsheet did not take into account reuse. He concluded with a request to 

not use the allocation spreadsheet provided in the report as the starting point for TMDL 

implementation. 

Response: The Department did not use the permitted load as the starting point because many 

facilities were discharging far below their permitted load and stakeholders recommended that 

we use the 1997–98 loadings with an allowance for anticipated growth over the next few years 

as the starting point for load reductions. The allowance for growth was site-specific and was 

based on discussions between Northeast District staff and individual permittees. The previous 

commitment by JEA to reduce nitrogen by 50 percent was not reflected in the allocation 

spreadsheet in the document because JEA requested a more equitable allocation. It is our 

understanding, however, that JEA will stand by its commitment and will negotiate with other 

parties in a form of pollutant trading. And finally, it is our intent to take reuse into account in the 

allocation process, and if the allocation failed to take reuse into account, we recommend that 

Captain Cotton raise the issue during development of the B-MAP for the TMDLs. 

Comments from Michael Wadel, Water Program Manager, 

Naval Air Station, August 28, 2003 

Mr. Wadel asked a variety of questions related to nonpoint sources and the wasteload 

allocation to Phase II MS4s (Municipal Separate Storm Sewer Systems). He was 

specifically concerned about how the WLAs were incorporated into the model, how the 

suggested nonpoint source reductions were allocated, and whether any additional 

reductions/BMPs required by the TMDL will be redundant with previously required 

stormwater treatment activities. 

Response: As noted in Section 6.3 of the document, the WLA for the estuarine portion of the 

river was a combination of the sum of the WLAs for all of the NPDES wastewater facilities and 

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the stormwater discharge from Duval County Municipal Separate Storm Sewer Systems 

(MS4s). To estimate the load from the Duval County MS4s, the urban stormwater component of 

the nonpoint source loads to the estuarine portions of the river (as estimated by the Pollution 

Load Screening Model) were moved from the nonpoint source inventory to the WLA. Consistent 

with the recommended allocation methodology, the TN load estimated for urban nonpoint 

sources was then reduced by the expected reduction that would be achieved through 

implementation of stormwater BMPs in 90 percent of the urbanized area. This description 

notwithstanding, we acknowledge that there is a lot of uncertainty in the estimation of nonpoint 

source loads and whether additional BMPs beyond the Maximum Extent Practicable will be 

required to implement WLAs for MS4s. Many of these issues will be discussed with 

stakeholders during B-MAP development. 

Comments from T. Niles Glasgow, State Conservationist, 

NRCS, August 29, 2003 

Mr. Glasgow commented that it was unclear how the allocation spreadsheets were 

developed, specifically in regard to reductions for agricultural operations which will vary 

by the type of agricultural operation. Mr. Glasgow also commented that the document 

did not include a monitoring/evaluation plan nor an Implementation Plan. 

Response: The reductions used for agricultural sources were based on documented reductions 

for TN and TP from BMPs developed for the Tri County Agricultural Area by the SJRWMD. As 

for the monitoring and implementation plan, these important elements of the overall TMDL 

process will be developed as part of the B-MAP. 

Comments from Neil Armingeon, St. Johns Riverkeeper, 

August 28, 2003 

Mr. Armingeon started his comment letter by expressing his gratitude to the Department 

for its inclusionary TMDL development process, commended the Department for 

initiating a process to reduce nutrient loading to the river, and commended the SJRWMD 

on its model development efforts. However, he expressed his concern with how the 

model was used to arrive at the TMDL, and had the following specific comments: 

(1) He expressed concerns about the chlorophyll a target for the freshwater 

portion of the river, commenting that allowing 10 percent of the values to be 

above 40 μg/L may allow a violation of the narrative nutrient criteria, that it 

would not be protective of filamentous algal blooms that could impact SAV 

populations, that it could still result in toxin production, and that it should be 

applied for a worst-case year rather than a long-term average. 

(2) He expressed concerns about the DO target used in the estuarine portion of 

the river, which was based on an EPA methodology for Cape Cod to Cape 

Hatteras, and requested that the Department develop site-specific alternative 

criteria (SSACs) for DO and then determine a new TMDL based on the SSAC. 

(3) He expressed concerns that the loading inventory did not include the 

“required” five-year growth projection and requested that this growth be 

evaluated as part of the TMDL rather than during BMAP development. 

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(4) He requested we add text to the document stating that the TMDL process will 

result in reductions from all nutrient sources. 

Responses: 

(1) The chlorophyll a target was specifically designed by the SJRWMD as a better interpretation 

of the narrative nutrient criteria than the annual average chlorophyll a value that is used to 

identify waters impaired by nutrients in the Impaired Surface Waters Rule (Rule 62-303, 

F.A.C.). As noted in the TMDL document, Hendrickson evaluated the maximum algal 

biomass levels that would (a) maintain diversity of the plankton community, (b) facilitate 

upward transfer of primary production to higher trophic levels (and maintain zooplankton 

diversity), and (c) minimize the potential of dominance of detrimental algal species and 

production of algal toxins. He found that a chlorophyll a target of 40 μg/L not to be 

exceeded more than 10 percent of the time would protect the aquatic flora and fauna of the 

river. Studies have shown that when chlorophyll a levels rise above 40 μg/L, a shift in algal 

types occurs: blue-green algae begin to dominate the system, toxic algal species begin to 

increase, and zooplankton communities begin to decline. As such, we do not expect 

filamentous blue-green algae or toxic algae once the reductions required by the TMDL are 

implemented. 

 The Department readily acknowledges that the current modeling effort was not designed to 

assess impacts on submerged aquatic vegetation (SAV). As we have discussed with 

stakeholders, the SJRWMD is actively working on a variety of studies that will allow the 

district to revise the model to address SAV impacts, and the Department plans to use the 

revised model to update the TMDL for the LSJR during the next basin management cycle. 

 Regarding application of the chlorophyll a threshold, the TMDL Stakeholders, TMDL 

Executive Committee, SJRWMD, and Department all agreed that it would be overly 

conservative to apply the threshold in a worst-case year and that a long-term average was 

adequately protective of the river. There were many reasons for this position, including the 

fact that there are already conservative elements of the modeling (applied in the worst-case 

WBID, for example), it is common practice for nutrient TMDLs to be based on “design runs” 

that estimate long-term average conditions, stormwater treatment design criteria and BMPs 

(the implementation of which will be how most of the nonpoint source reductions will be 

achieved) are typically designed for rain events that would not be typical of the worst-case 

year, and external load model estimates of nonpoint source loading would overestimate 

loading for dry years because they would not adequately take into account the increased 

removal provided by stormwater treatment facilities. Nutrient management activities for 

nonpoint sources will naturally be more effective at dry conditions such that additional 

nonpoint source reductions required for a worst-case dry year are not needed and would 

result in the overdesign of stormwater facilities. 

(2) The Department is confident that the DO threshold developed by the SJRWMD more 

accurately reflects conditions at which low DO levels would impact aquatic life use support 

than the current state DO criterion and plans to develop either a SSAC for the area or 

perhaps revise the statewide criteria using the EPA methodology.

(3) It should be noted that there is no requirement to include a 5-year growth projection in the 

TMDL. We assume Mr. Armingeon is referring to the Allocation Technical Advisory 

Committee recommendation to include a 5-year projection for growth when allocating 

TMDLs. We agree with this recommendation, and the SJRWMD made some preliminary 5-

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year growth projections by extrapolating growth over the last 10 years. However, the 

Stakeholders Committee and TMDL Executive Committee recommended that the 

Department use actual growth projections from the Northeast Florida Regional Planning 

Council instead. As it turned out, the projections were not ready by the time the TMDL was 

due to be submitted to the EPA, and it was decided that growth projections would be 

addressed during BMAP development. Any increased nonpoint source load from future 

growth will need to be offset by reductions in current nonpoint source loadings. 

(4) The TMDL allocation spreadsheet in the appendix was revised to reflect reductions at all 

facilities, rather than just JEA facilities. However, we do not agree with Mr. Armingeon’s 

position that all sources should be required to reduce their loadings by the same percent. 

Our allocation strategy tries to equitable allocate load reductions by taking prior treatment 

into account and allows for informal pollutant trading—both of which will be addressed 

during BMAP development. 

Response from Jim Maher, Northeast District Office, August 

19, 2003 

Mr. Armingeon also indirectly provided comments to the Department in the form of an email to Riverkeeper Members, which include some Department staff. Attached below is a 

copy of a response to that e-mail from Jim Maher (Northeast District), which provides 

responses to the issues raised in Mr. Armingeon’s e-mail (Mr. Armingeon’s comments 

are shown in bold italics). 

From: Maher, Jim 

Sent: Tuesday, August 19, 2003 4:39 PM 

To: 'Breen, Katherine'; Armingeon, Neil 

Subject: RE: RIVER ISSUE 

Good Morning Riverkeepers 

Per my discussion with Neil yesterday, I would appreciate your forwarding my comments to the 

membership if you still see fit to do so. Thank you very much for the opportunity. 

Dear Riverkeeper Member, 

As a fellow Riverkeeper member and also a DEP employee who has been working on the 

TMDL for some time, I'd like the chance to add to and address the issues Neil outlined in a 

recent email. Under the direction of Jerry Owen, our Water Facilities Administrator, we here at 

the DEP have been working closely with the Riverkeeper, the St. Johns River Water 

Management District and many other stakeholders in monthly meetings for more than a year 

now to help shape this TMDL to be the most scientifically accurate and environmentally useful 

tool ever developed to date to reduce the nutrient enrichment in the St. Johns. Thanks to 

insightful contributions from the Riverkeeper, the Stewards of the St. Johns and other 

stakeholders, we have made many changes that strengthen the TMDL and make it more 

effective. This is what community consensus does best. Our District Director, Mario Taylor, has 

elevated working with the stakeholders and executives from all affected groups to a high priority. 

Some of the issues that Neil outlined have been improved thanks to your collective input. That 

may not have been well communicated yet as some of the changes were fairly recent, so please 

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allow me to show how we currently do address these important concerns, taken in order as Neil 

presented them: 

the proposed TMDL: - does not require a reduction of nitrogen from upstream, the largest 

source of nitrogen pollution in the lower St. Johns; 

The TMDL as modelled and as shown in a draft allocation strategy does indeed apply the same 

reduction in fresh water section (30 percent) to the total of the nutreint load coming from 

upstream. The load from upstream will have to be reduced to meet their share of the nutrient 

reduction responsibility. Modelling shows that this, along with the reductions within the basin 

will eliminate the severe algae blooms and species shift from good algae to undesirable species 

which is indicative of an unhealthy system. 

- does not take into account planned growth and development; 

This is true for what has been presented so far, but we have only just received growth and 

development estimates from the Northeast Florida Planning Council (requested by the 

stakeholder meetings) and the very next computer run the Water Mangement District does of 

the river modelling WILL include the growth and development. This was an important issue for a 

number of the stakeholders, including agriculture, and the process is improved with this 

addition. While adding this to the next computer run may alter who has to reduce what by how 

much, the total reduction requirement will be unchanged, and that is what is being proposed in 

the actual TMDL, what must the Total Load get down to. HOW we get down to it will be the 

subject of Basin Management Action Plan (BMAP) discussions over the next year, which will 

also heavily rely on community input. But what we're legally dealing with right now is the total 

load to get down to, and it will be the same, even if loads from new growth prompts additional 

reductions elsewhere. 

- does not consider the possibility of using the St. Johns River as a source for drinking 

water; if this occurs, the River's volume will be reduced and may not be able to 

effectively absorb the nitrogen; 

We don't have any projections that this will occur during the next 5 year period. The TMDL will 

be revised on a 5 year cycle. If we have information that this is going to happen in the next year 

cycle, it will be included in the model's projections. 

and is not fair. The amount of reduction is not the same for all sources of nitrogen. 

This is another example of how the process has been improved due to stakeholder input. The 

inital draft allocation relied only on some large facility reductions in the marine section. In 

response to Riverkeeper and other stakeholder calls for a more fair allocation, the draft strategy 

has been changed to require every point source to get dowm to the same level of treatment. 

1. The TMDL should be based upon EPA approved water quality standards; 

While there are no numeric standards for nutrients, the narrative standard of not causing an 

imbalance of flora and fauna has been translated by Water Management District researchers 

with cutting edge scientific development. I submit the work done by key WMD scientists rivals 

that done any where else in the country. The tools they have developed and incorporated into 

the model and evaluative process are so sophisticated and are more intricate than the work 

done anywhere else, save perhaps the Everglades. The St. Johns is an intricate, complex 

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system that behaves like a lake sometimes, a stream others, and has tidal exchange 100 miles 

inland. There is nothing else like it, so the evaluative requirements are complex and 

demanding. These folks have risen to the occasion. 

That said, one of the translations of the nutrient criteria identifies Dissolved Oxygen (DO) sags 

as evidence of enrichment due to the oxygen demand of algal detritus, or decaying dead algae. 

This indirect use of Dissolved Oxygen actually identifies appropriate oxygen sags between 3.2 

mg/L and 4.8 mg/L, depending on length of the sag. While we believe this to be appropriate for 

the system, and it was originally borrowed from an EPA generated oxygen limit profile for 

another waterbody, it is less than the non-site specific criteria of 5 mg/L we have in Florida 

Administrative Code (FAC) that has been approved by EPA for all of Florida. EPA can approve 

a site-specific alternative criteria (SSAC) of less than 5 if it is appropriate for the system. The 

WMD researchers have provided compelling evidence that this range is appropriate for the St. 

Johns given our species composition, physical characteristics and dark water. The case was 

presented at stakeholders meetings and will be used to officially obtain and SSAC for EPA. 

While this process takes a while, we will pursue it concurrently with the TMDL and believe, with 

all stakeholder input, including other scientists in regulatory agencies and outside government, 

that it is the correct thing to do. 

2. The proposed TMDL will continue to allow harmful algae blooms which can be toxic to 

humans and aquatic life; 

We believe that if the reductions projected to be required from these scientists' work can truly be 

implemented (our next great challenge), the harmful algae blooms won't be allowed to continue. 

Of course there are no guarantees, but if these efforts don't do the trick, we'll have to cut deeper 

in the next cycle. But the greater task at hand is ensuring that we can implement this much. 

The point sources should be no problem as we can put their requirements into their permits. 

But without public funding and project support, getting this level of nutrient reductions in nonpoint source runoff and upstream will be doomed. WE NEED YOUR HELP HERE! 

3. The TMDL ignores growth and development occurring in the lower St. Johns area; and 

As mentioned above, we have numbers from the planning council to update the model input and 

work this out in the allocation process. We invite all concerned to look at those inputs and 

ensure they accurately reflect expected growth and development, but again that will be an 

allocation issue and won't affect the total load we must get down to. 

4. If a 20 -30 percent reduction is the target, all sources of nitrogen pollutants, not a 

select few, should be required to reduce their discharges by that percentage. 

All sources will now have to share in the pain, thanks to changes made by your Riverkeeper's 

insistence. However, for those facilities that have already made treatment upgrade investment, 

they may have to only reduce a lesser amount than those who currently have no nutrient 

reduction treatment at all, so that everybody gets down to the same level of treatment efficiency. 

This is the most fair way (and the only physically possible way) to do this, and I know that is 

your intent. 

Neil is right, this is YOUR River and only with your help and participation can we provide the 

protections and restorations it needs. This is why the Riverkeeper group, as well as the 

Stewards of the St. Johns and other river advocacy groups must remain strong, and your voice 

must be heard, so please keep supporting them and stay involved. Let your representatives 

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know that protecting the river is your priority and insist adequate resources be provided to 

implement this TMDL. With your voice we can heal the river together. 

Jim Maher 

Comments from Riverkeeper Members 

Mr. Armingeon’s e-mail resulted in approximately 21 e-mails from Riverkeeper members 

that echoed the same four concerns: (1) the TMDL should be based upon EPA-approved 

water quality standards, (2) the proposed TMDL will continue to allow harmful algae 

blooms that can be toxic to humans and aquatic life, (3) the TMDL ignores growth and 

development occurring in the lower St. Johns area, and (4) if a 20 to 30 percent reduction 

is the target, all source of nitrogen pollutants, not a select few, should be required to 

reduce their discharges by that percentage. 

Response: Mr. Maher’s e-mail addressed all four issues, and several additional issues. 

Comments from the St.Johns Riverkeeper Provided at the 

TMDL Adoption Hearing 

Mr. Armingeon provided additional comments in writing at the TMDL adoption hearing on 

September 30, 2003. The comments reiterated his previous comments on the chlorophyll 

a target, the DO target, and the five-year growth projections, but he added some 

additional detail based on his review of the files at the SJRWMD. Mr. Armingeon 

commented that this review strengthened his belief that the TMDL would not protect the 

biological integrity of the system and will allow continued degradation of the LSJR. He 

included the following specific recommendations: 

1. Consider water column light attenuation that is deleterious to SAV when 

establishing chlorophyll a levels. 

2. Correlate chlorophyll a standards with SAV growing season and periods of low 

DO due to high water temperatures. 

3. Establish continuous monitoring DO meters in the estuaries and freshwater 

portions of the river. Reassess DO impairment in these sections. 

4. Determine the effect of phytoplankton levels on total suspended solids load in 

the oligohaline reach of the river. 

5. Reduce the chlorophyll a target to levels below current ambient levels. 

6. Reevaluate nutrient levels relative to littoral zone filamentous algal loads. 

7. Investigate the environmental factors driving the production of algal toxins and 

their potential relationship to nutrient enrichment. 

Response: We had previously addressed most of Mr. Armingeon’s comments and 

recommendations, but it should be noted that the TMDL is based on the worst-case WBID 

rather than the average chlorophyll for the river, and the worst case WBIDs currently have 

chlorophyll a values well above 40 μg/L (see Recommendation 5). 

 74 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix I: Annual Average Chlorophyll a Values and 

TSIs for the LSJR Main Stem 

WBID Waterbody Segment Chla or TSI1 Annual Average Chlorophyll or TSI 

for Given Year

1996 1997 1998 1999 2000 2001 

2213A STJ RIV AB MOUTH Chla NA2 NA NA NA 4.42 4.67 

2213B STJ RIV AB ICWW Chla 4.65 3.52 10.31 8.40 7.21 9.79 

2213C STJ RIV AB DAMES PT Chla 4.35 3.61 NA 6.12 4.54 7.89 

2213E STJ RIV AB WARREN BRG Chla 9.02 12.31 14.98 12.0 9.21 8.55 

2213F STJ RIV AB PINEY PT Chla 7.50 NA 14.89 9.31 12.55 6.16 

2213I STJ RIV AB BLACK CK TSI 61.4 61.5 62.6 58.6 56.2 57.8 

2213J STJ RIV AB PALMO CK TSI 63.6 63.0 64.1 61.6 56.3 59.7 

2213K STJ RIV AB TOCIO TSI 66.0 64.6 64.5 66.0 63.4 63.9 

2213L STJ RIV AB FEDERAL PT TSI 65.4 63.6 62.2 64.7 60.9 60.4 

2213M STJ RIV AB RICE CK Chla 31.14 30.06 25.09 37.79 25.07 25.23 

2213N STJ RIV AB DUNNS CK Chla 34.04 31.81 21.30 31.42 24.40 NA 

1

 Chlorophyll in μg/L and TSI unitless. 2

 NA = Not available. 

3 Listed based on increase over historical levels. 

 75 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix J: Allocation Spreadsheets for the 

Freshwater and Estuarine Portions of the LSJR 

Wasteload and Load Allocations for Freshwater Portion of River – 

Total Phosphorus (kg/yr) 

Source Category or Name of Facility 

Wasteload 

Allocation 

(kg/yr) 

Required 

Percent 

Reduction 

 

Point Sources - Wastewater 

Georgia-Pacific 33,181.8 48.05% 

Palatka WWTF 6,669.5 33.00% 

Green Cove Springs - Harbor1 1,851.5 38.00% 

Green Cove Springs - South1 545.2 38.00% 

Future Apricot/RO Dischargers 3,320.1 0.00% 

 

Point Sources - MS4s2 

Green Cove Springs1 575.9 47.44% 

Clay County 212.6 47.44% 

 

Load Allocations2 

Agriculture 70,974.2 14.96% 

Non-MS4 Stormwater2 

Putnam County 3,964.9 33.81% 

Palatka 792.5 47.44% 

St. Johns Co. 3,296.6 11.56% 

Clay Co. non-MS4 499.4 34.92% 

Welaka 90.4 47.44% 

Hastings 49.3 46.93% 

Pomona Park 15.8 0.00% 

Alachua County 83.8 0.00% 

Flagler Co. 0.9 0.00% 

 

Atmospheric Deposition 1,355.9 0.00% 

1

 Green Cove Springs has requested that its MS4 and wastewater loads be aggregated into one WLA, 

which would be 2,972.6 kg/yr. 

2

 Loads shown for MS4s and non-MS4s are provided only for the purposes of pollutant trading and 

aggregation of loads. The allocations are expressed in percent reduction. 

 76 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Freshwater Portion of River – Nitrogen (kg/yr) Average of 

95,97,98,99 

Source Category or Name of Facility Allocation Net Reduction from 

Current 

Point Sources - Wastewater 

Georgia-Pacific 165,909.1 35.73% 

Palatka WWTF 40,795.4 33.00% 

GCS Harbor1 5,863.2 38.00% 

GCS South1 3,188.8 38.00% 

Seminole Electric 4,006.7 30.00% 

Future Apricot/RO Dischargers 9,960.5 0.00% 

Point Sources - MS4s2

Green Cove Springs1 4,986.6 28.37% 

Clay County 1,984.2 28.37% 

Load Allocations2

Agriculture 195,120.2 37.20% 

Non-MS4 Stormwater2

Putnam County 34,113.4 21.79% 

St. Johns Co. 25,442.2 6.73% 

Palatka 6,936.1 28.37% 

Clay Co. non-UA 4,418.5 20.80% 

Welaka 841.4 28.37% 

Hastings 449.4 28.03% 

Alachua Co. non-UA 0.0 0.00% 

Pomona Park 107.9 0.00% 

Flagler Co. non-UA 6.9 0.00% 

Atmospheric Deposition 105,688.2 0.00% 

1

 Green Cove Springs has requested that its MS4 and wastewater loads be aggregated into one WLA, 

which would be 14,038.6 kg/yr. 

2

 Loads shown for MS4s and non-MS4s are provided only for the purposes of pollutant trading and 

aggregation of loads. The allocations are expressed in percent reduction. 

 77 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Marine Portion of River – Nitrogen (kg/yr) 99 

Source Category or Name of Facility Allocation Net Reduction from Start Point 

Point Sources - Marine Wastewater 

An Busch - Mn St 12,413.4 49.12% 

Atl Beach - Buccanneer2 8,428.5 60.00% 

Atl Beach - Main2 13,425.9 52.40% 

CCUA - Fleming Island4 43,820.5 -53.56% 

CCUA - Fleming Oaks4 2,983.5 -78.05% 

CCUA - Miller St4 37,219.5 -18.70% 

Jax Beach WWTF1 23,868.2 40.55% 

JEA - Arlington3 134,258.7 62.24% 

JEA - Beacon Hiils3 7,384.2 55.04% 

JEA - Brierwood SD3 0.0 0.00% 

JEA - Buckman3 253,748.9 48.43% 

JEA - District II3 40,277.6 76.11% 

JEA - Holly Oaks3 0.0 0.00% 

JEA - Jax Heights3 12,083.3 46.45% 

JEA - Jul Crk3 3,550.4 55.42% 

JEA - Mandarin3 52,211.7 -0.87% 

JEA - Monterey3 26,851.7 52.54% 

JEA - Ortega Hills3 0.0 0.00% 

JEA - Royal Lakes3 22,301.9 30.35% 

JEA - San Jose3 16,782.3 46.19% 

JEA - San Pablo3 5,594.1 15.71% 

JEA - St. Johns North3 0.0 0.00% 

JEA - SW3 74,588.1 48.62% 

JEA - Woodmere3 4,773.6 52.83% 

Neptune Beach WWTF5 7,011.3 38.75% 

Orange Park WWTF6 9,994.8 59.84% 

Smurfit - Jax 0.0 0.00% 

Smurfit-Stone Container 74,274.6 49.12% 

USN - Mayport WWTF7 7,682.6 44.94% 

USN - NAS Jax WWTF7 8,428.5 36.50% 

Westminster Woods 0.0 0.00% 

Future Apricot/RO Dischargers 4,979.3 0.00% 

JEA Total 654406.5 53.14% 

CCUA - Total 84,023.5 -36.47% 

Point Sources - MS4s8

Atlantic Beach 975.4 60.57% 

Clay_marine_UA 10,551.8 58.21% 

NAS Jax 1,769.1 62.86% 

 78 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Source Category or Name of Facility Allocation Net Reduction from Start Point 

Point Sources - MS4s8

Jacksonville,City 95,977.0 60.57% 

Jax Beach 1,940.0 61.00% 

SJ Co 4,537.3 56.82% 

Orange Park 1,288.9 62.65% 

Mayport UA 1,027.9 62.85% 

Neptune Beach 585.2 60.57% 

Load Allocations8

Agriculture 4,167.8 67.44% 

Non-MS4 Stormwater8

Clay_marine_nonUA 4,973.4 58.73% 

Camp Blanding 1,572.8 58.61% 

SJC remaining marine 1,060.1 55.29% 

Penney Farms 163.0 0.00% 

Atmospheric Deposition - Marine 95,028.1 0.00% 

1

 Jacksonville Beach requested that its MS4 and wastewater loads be aggregated into one WLA, which would be 

25,808.2 kg/yr . 

2

 Atlantic Beach requested that its wastewater loads be aggregated into one WLA, which would be 22,829.7 kg/yr. 

3

 JEA requested that all its wastewater allocations be aggregated into one WLA, which would be 654,406.5 kg/yr. 

4

 Clay County Utilities Authority requested that its wastewater allocations be aggregated into one WLA, which would be 

84,023.5 kg/yr. 

5

 Neptune Beach requested that its wastewater allocations be aggregated into one WLA, which would be 7,596.5 kg/yr. 

6

 Orange Park requested that its wastewater allocations be aggregated into one WLA, which would be 11,283.8 kg/yr. 

7

 The United States Navy requested that its wastewater allocations be aggregated into one WLA, which would be 

18,908.0 kg/yr. 

8

 Loads shown for MS4s and non-MS4s are provided only for the purposes of pollutant trading and aggregation of loads. 

The allocations are expressed in percent reduction. 

 79 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix K: Ongoing and Proposed Studies by the 

SJRWMD Designed To Revise the TMDL To Address 

Submerged Aquatic Vegetation and Further Evaluate 

Nutrient Impacts in the Lower St. Johns 

The list below summarizes some of the key projects. It is not intended to identify all of the 

ongoing projects and programs that are part of the SJRWMD activities in the LSJR and its 

designation as a SWIM water at the state level or an American Heritage River at the federal 

level. 

1. The SJRWMD recently amended its contract with the USACE/WES to add money to 

complete necessary code changes in the SAV components of CE-QUAL-ICM, improve 

model simulation speed by parallel processing of grids, and set up a sigma grid option. The 

contract is scheduled to be completed by the end of the year (2004). 

2. Dr. Carl Gallegos is completing further work on his light model for the St. Johns by 

addressing salinity influences. A final report is due at the end of the year (2004). 

3. Dr. Hans Paerl has one more year of field studies to complete his three-year study on 

nitrogen fixation in the LSJR. This summer, he will conduct monthly surveys and three oneweek assays. A final report is due next March (2005). 

4. Funding for Dr. Ed Philps’ phytoplankton and zooplankton sampling was extended for two 

more years. He will conduct some studies in conjunction with Dr. Paerl this summer. 

5. The SAV project with the U.S. Geological Survey lab in Louisiana was completed and final 

reports should be available this summer (2004). Information obtained through those studies 

will be used in the CE-QUAL-ICM model. 

6. A contract was recently signed with researchers at the University of Alabama to study the 

export and degradation of terrestrially derived organic material in the LSJR. 

7. An ongoing project that has evaluated sediment fluxes and denitrification rates will continue 

through the fall and will involve monthly sampling during this summer. The results of this 

work will be used to review rates that were used in the model to establish the TMDL. 

 80 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix L: Site-Specific Alternative Dissolved 

Oxygen Criterion Documentation 

 81 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

 82 

Florida Department of Environmental Protection 

Site Specific Alternative 

Dissolved Oxygen Criterion 

to Protect Aquatic Life in the 

Marine Portions of the 

Lower St. Johns River 

Technical Support Document

April 28, 2006 

Prepared by: 

Florida Department of Environmental Protection 

Tallahassee, FL 

& 

St. Johns River Water Management District 

Palatka, FL 

For Submittal to: 

U.S. Environmental Protection Agency 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

 83 

Florida Department of Environmental Protection 

Table of Contents 

Page

INTRODUCTION ........................................................................................................... 84 

Description of Existing Conditions...................................................................... 84 

OVERVIEW OF THE EPA VIRGINIAN PROVINCE DO CRITERIA APPROACH ........ 87 

Juvenile and Adult Survival ................................................................................. 87 

Growth .................................................................................................................... 88 

Larval Recruitment ................................................................................................ 88 

Application of the Marine Criteria Approach ...................................................... 91 

APPLICATION OF THE EPA VIRGINIAN PROVINCE APPROACH TO THE LSJR ... 92 

Derivation of the Proposed SSAC for DO in the LSJR ....................................... 94 

Final Proposed SSAC for DO in the LSJR ........................................................... 96 

LITERATURE CITED .................................................................................................... 98 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Introduction 

The purpose of this report is to provide the technical basis for establishing Site Specific 

Alternative Criteria (SSAC) for dissolved oxygen (DO) for the protection of aquatic life in the 

predominately marine portions of the Lower St. John’s River (LSJR) between Julington Creek 

and the mouth of the river. The SSAC for DO in the LSJR presented herein was developed in 

accordance with the procedures set forth in subsection 62-302.800(2), Florida Administrative 

Code, for Type II Site Specific Alternative Criteria. The proposed DO SSAC was derived by the 

Florida Department of Environmental Protection (FDEP) and the St. John River Water 

Management District (SJRWMD) based on an application of the methodology developed by the 

U.S. Environmental Protection Agency (EPA) for the Virginian Province (EPA 2000). As 

described below, EPA’s Virginian Province approach uses knowledge regarding the biological 

response of sensitive aquatic organisms to hypoxic stressors to derive DO criterion that provide 

adequate protection from acute and chronic effects of exposure to low DO levels in marine 

waters. 

Description of Existing Conditions 

Persistent, low (below 5 mg/L) concentrations of dissolved oxygen in the meso/polyhaline 

reach of the LSJR are well documented but poorly understood phenomena (Hendrickson, et al. 

2003). The incidences of low dissolved oxygen conditions occur simultaneous with high 

summertime temperatures, and appear to be associated with the decline of significant algal 

blooms. The U.S. Geological Survey has established continuous monitoring stations within the 

marine reach of the LSJR at Dames Point and the Acosta Bridge (Figure 1). Monitoring data 

from these two stations are available for the period from 1996 through 2001 and are 

summarized in Table 1. For the period of record, dissolved oxygen levels were below 5 mg/L 

for 0.5, 2.7, and 3.9 % percent of the time, in the surface, mid depth waters, and bottom, 

respectively, at the Acosta Bridge Station (Figure 2). Further downstream at the Dames Point 

site, DO concentrations were below 5.0 mg/L for 15% of the time at the surface, 22% of the time 

at mid depth, and 35% of the time at the bottom during the same period. 

Table 1. Summary statistics for daily dissolved oxygen concentrations (mg/L) 

measured at USGS automated monitoring stations at Acosta Bridge and Dames Point 

between 1996 and 2001 

Station Depth N Mean Median Std 

Dev. Minimum 25th Percentile 

75th 

Percentile Maximum 

Acosta 

Bridge 

Surface 918 7.4 7.3 1.27 3.7 6.4 8.3 11.0 

Middle 1059 7.0 6.9 1.26 2.9 6.1 7.8 11.0 

Bottom 1049 6.8 6.6 1.21 3.7 5.9 7.6 10.9 

Dames 

Point 

Surface 839 6.2 5.9 1.21 3.7 5.3 7.1 9.5 

Middle 808 5.8 5.6 1.19 3.2 5.0 6.5 9.2 

Bottom 707 5.6 5.4 1.11 3.4 4.7 6.3 9.0 

 84 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure 1. USGS water quality monitoring stations in the estuarine reach of the 

Lower St. Johns River 

 85 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

 86 

Florida Department of Environmental Protection 

0

10

20

30

40

50

60

70

80

90

100

Dissolved Oxygen (mg/L)

2 3 4 5 6 7 8 9 10 11 12

Frequency (%)

0

10

20

30

40

50

60

70

80

90

100

Dissolved Oxygen (mg/L)

2 3 4 5 6 7 8 9 10 11 12

A

B

Surface

Mid Depth

Bottom

Frequency (%)

Figure 2. Cumulative DO frequency distribution at the USGS (A) Acosta Bridge and 

(B) Dames Point stations from 1996 through 2001. The red vertical line 

indicates the current one day average Class III marine criteria of 5.0 mg/L.
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Overview of the EPA Virginian Province DO Criteria 

Approach 

The EPA Virginian Province document (EPA 2000) recommends an approach for deriving 

dissolved oxygen levels necessary to protect coastal and estuarine organisms in the Virginian 

Province. The document also provides guidance regarding the application of the recommended 

methodology to other coastal or estuarine systems. The proposed DO SSAC presented herein 

was derived based on an application of the methodology developed by the U.S. Environmental 

Protection Agency (EPA) for the Virginian Province (EPA 2000) to the Lower St. Johns River. 

The EPA Virginian Province methodology represents a synthesis of current knowledge 

regarding biological responses to hypoxic stressors in aquatic ecosystems. This approach 

considers the response to both continuous and cyclic exposures to low DO levels in the 

derivation of criteria which are protective of aquatic life. The aquatic life based approach utilized 

for the Virginian Province (EPA 2000) identifies three important DO concentration levels as 

follows: 

• The Criterion Continuous Concentration (CCC), which is defined as a mean daily DO 

concentration above which continuous exposure is not expected to result in 

unacceptable biological effects. 

• The Criterion Minimum Concentration (CMC), which is defined as a daily DO 

concentration below which any exposure for a 24-hour period would result in 

unacceptable acute effects (mortality). The CMC applies a lower limit for continuous 

exposures by using the final acute value (FAV) calculations outlined in Stephen et. al. 

(1985). 

• A set of mean daily DO concentrations between the CCC and CMC that identify 

conditions that may be tolerated for specific limited durations as defined by the Final 

Recruitment Curve (FRC). 

Aquatic life and its uses are assumed to be fully supported as long as DO conditions remain 

at or above the (CCC) chronic criterion for growth (EPA value = 4.8 mg/L). Conversely, if DO 

conditions fall below the juvenile/adult survival criterion (CMC) of 2.3 mg/L (EPA value), there is 

insufficient DO to prevent unacceptable effects to aquatic life. When DO conditions are 

between these two values (2.3 to 4.8 mg/L), further evaluation of the duration and intensity of 

low DO is needed to determine whether the level of oxygen can support a healthy aquatic life 

community (EPA 2000). This evaluation is conducted via comparison between monitored data 

and the FRC. To derive the CCC, CMC, and FRC, the EPA Virginian Province method utilizes 

biological responses of sensitive species during various life stages to low DO concentrations as 

briefly summarized below. 

Juvenile and Adult Survival 

Data regarding the acute sensitivity of juvenile and adult saltwater organisms to continuous 

low DO exposures ranging from 24 to 96 hours were used to derive the Criterion Minimum 

Concentration (CMC) in EPA’s Virginian Province method. Acute response data were available 

for 12 invertebrate and 11 fish species (Table 2). 15 of the 23 species used by EPA for the 

Virginian Province are also known to inhabit estuarine waters of northeast Florida based on 

sampling and expert knowledge (Hendrickson, et al., 2005; FMRI 2002; CSA, Inc., 1993; 

 87 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Frydenborg 2005). The species known to be indigenous in Florida generally span the range of 

acute DO sensitivities and include the most sensitive species (pipe fish, Syngnathus fuscus) 

used by EPA (Table 2). 

EPA calculated the criteria for exposure to continuous low DO by using a modified version of 

the procedure for the derivation of a final acute value (FAV) for toxicants presented in Stephen 

et al., (1985). The standard procedure was modified to account for the fact that organisms 

respond to DO in an opposite manner than that to toxicants; that is, the greatest negative 

response is low levels rather than high levels. The FAV for the Virginian Province was 

calculated to be 1.64 mg/L, which is the value representative of the LC50 for the 95th percentile 

genus (as ranked in order of sensitivity to low DO levels). The FAV was then adjusted to a 

CMC of 2.27 mg/L by multiplying by the average LC5 to LC50 ratio (1.38) for juveniles. 

Similarly, a CMC of 2.3 mg/L was derived by Hendrickson et al., (2003) based on a calculation 

performed using the 12 species known to inhabit the study area and based upon the FAV for the 

most sensitive species (pipe fish). 

Growth 

To protect against sub-acute effects, the Virginian Province DO criteria also included an 

evaluation of the effect of low DO levels on marine organism growth. EPA (2000) noted that 

growth is generally more sensitive to low DO than survival, although the document does 

mention exceptions for Menidia menidia and Dyspanopeus sayi where survival was the more 

sensitive endpoint in some tests. 

EPA (2000) evaluated data on the effects of low DO on the growth of 11 species (4 fish and 

7 invertebrates) from a total of 36 tests. Geometric mean chronic values (GMCV) for the 11 

species ranged from 1.97 mg/L (sheepshead minnow,Cyprinodon variegatus) to 4.67 mg/L 

(longnose spider crab, Libinia dubia). A DO level protective of growth was determined to be 4.8 

mg/L, which represented the chronic value that would not result in a greater than 25 percent 

reduction in growth in species at the 95th percentile of the values for sensitive species 

represented. Long-term, continuous exposures at or above this level should not cause 

unacceptable effects to marine organisms. 

Larval Recruitment 

U.S. EPA (2000) developed a generic model to evaluate the cumulative effect of low DO on 

early life stages of aquatic animals. This model was used to estimate the effects of DO 

concentrations between the acute value (CMC) of 2.3 mg/L and the CCC (4.8 mg/L). The 

model used for the Virginian Province estimates the duration a DO concentration can be 

tolerated without causing unacceptable effects on larval recruitment, defined as greater than 5% 

reduction in larval recruitment during the entire recruitment season. A final recruitment curve 

(FRC) was developed between the CCC and CMC. 

The FRC was fit using the larval dose-response curves from the four most sensitive genera 

(Morone, Homarus, Dyspanopeus, and Eurypanopeus). The equation for the FRC was derived 

by fitting the line of best fit through the points generated by output of the recruitment model 

(Figure 2). The equation for the FRC is given as: 

)PL(eP

LP P(t) Lkt

0

0 −+ 0

= −

 88 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

 89 

Florida Department of Environmental Protection 

where: P(t) = the DO concentration at time t 

 P0 = the y-intercept 

 L = the upper DO limit 

 k = a rate constant, and 

 t = time in days, the number of days over which P(t) may be tolerated 

EPA (2000) and Thursby (2003) suggested that the FRC developed for the Virginian 

Province may be overprotective for areas to the south. This is due to the fact that recruitment 

seasons lengthen and larval development times decrease, with increased distance south from 

the Virginian Province. Both factors would act to decrease the sensitivity of the FRC and shift 

the curve in Figure 2 down and to the right. 

Figure 2. Plot of model outputs that protect against greater than a 5% 

cumulative impairment of larval recruitment. The solid line is 

regression of best fit for the FRC based on the 4 most sensitive 

species. Figure taken from EPA (2000). 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Table 2. Acute sensitivity of juvenile and adult saltwater animals to low dissolved oxygen. Exp

ranged from 24 to 96 hr. (Re-created from EPA 2000). Highlighted species are known tto the St. Johns River. 

Species Common Name Life Stage SMAV LC50a SMAV LC5 SMAV LC5/LC50 GMAV LC50 GMAV LC50a GMA

LC5 

Carcinus maenus Green Crab Juvenile/Adult <0.34 <0.34 0.34 Spisula solidissima Atlantic Surf Clam Juvenile 0.43 0.7 1.63 0.43 0.43 0.70 Rithropanopeus harrisii Harris Mud Crab Juvenile 0.51 0.51 0.51 Prionotus carolinus Northern Sea Robin Juvenile 0.55 0.8 1.45 0.55 0.55 0.80 Eurypanopeus depressus Flat Mud Crab Juvenile 0.57 0.57 0.57 Leiostomus xanthurus Spot Juvenile 0.7 0.81 1.16 0.7 0.7 0.81 Tautoga onitis Tautog Juvenile 0.82 1.15 1.40 0.82 0.82 1.15 Palaemonetes vulgaris Marsh Grass Shrimp Juvenile 1.02 1.4 1.37 0.86 0.86 1.24 Palaemonetes pugio Daggerblade Grass Shrimp Juvenile 0.72 1.1 1.53 Ampelisca abdita Amphipod Juvenile <0.9 <0.9 0.9 Scopthalmus aquosus Windowpane Flounder Juvenile 0.81 1.2 1.48 0.9 0.9 1.20 Apeltes quadracus Fourspine Stickleback Juvenile/Adult 0.91 1.2 1.32 0.91 0.91 1.20 Homarus americanus American Lobster Juvenile 0.91 1.6 1.76 0.91 0.91 1.60 Crangon septemspinosa Sand Shrimp Juvenile/Adult 0.97 1.6 1.65 0.97 0.97 1.60 Callinectes sapidus Blue Crab Adult <1.0 <1.0 1 Brevoortia tyrannus Atlantic Menhaden Juvenile 1.12 1.72 1.54 1.12 1.12 1.72 Crassostrea virginica Eastern Oyster Juvenile <1.15 <1.15 1.15 Stenotomus chrysops Scup Juvenile 1.25 1.25 1.25 Americamysis bahia Mysid Juvenile 1.27 1.5 1.18 1.27 1.27 1.50 Paralichthys dentatus Summer Flounder Juvenile 1.32 1.57 1.19 1.32 1.32 1.57 Pleuronectes americanus Winter Flounder Juvenile 1.38 1.65 1.20 1.38 1.38 1.65 Morone saxatilis Striped Bass Juvenile 1.58 1.95 1.23 1.58 1.58 1.95 Syngnathus fuscus Pipe Fish Juvenile 1.63 1.9 1.17 1.63 1.63 1.90 

a SMAVs (Species Mean Acute Values) and GMAVs (Genus Mean Acute Values) Final Acute Value = 1.64 

 are all geometric mean values (Stephen et al., 1985) Mean LC5/LC50 Ration = 1.38 

CMC = 1.64 mg/L x 1.38 = 2.27 

b Ranked according to LC50 GMAV values 

 90 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Application of the Marine Criteria Approach 

The final marine DO criteria for the Virginian Province are summarized in Figure 3. Below the 

survival level (CMC=2.3 mg/L), DO does not meet protective goals and designated uses are not 

maintained. At DO levels above the CCC growth level (4.8 mg/L) unacceptable effects from 

exposure to low DO levels are not expected and aquatic life and its uses are adequately 

protected. Evaluation of DO levels between the survival and chronic protection levels is based 

on the comparison between the FRC and measured cumulative DO exposure durations. sure durations. 

Figure 3. Plot of the final Virginian Province DO criteria for marine animals 

continuously exposed to low dissolved oxygen. 

1.5

2.0

2.5

3.0

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75

Exposure Time (days)

Dissolv

3.5

4.0

4.5

5.0

5.5

ed Oxygen (mg/L)

Final Larval Recruitment Curve

Growth CCC = 4.8 mg/L

Juvenile Survival CMC = 2.3 mg/L

 91 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Application of the EPA Virginian Province Approach 

to the LSJR 

The FDEP and SJWMD have evaluated the Virginian Province approach for deriving DO 

criteria for possible application in Florida’s marine waters where the existing criteria may not be 

appropriate. Because the EPA’s recommended approach for the Virginian Province is based on 

very conservative assumptions for northern cooler waters, it can be concluded that application 

of a similar approach to derive DO criteria for Florida’s marine waters would provide a very 

conservative level of protection for aquatic life. In addition, many of the species used to derive 

the Virginian Province criteria are also known to occur in Florida waters including the LSJR with 

the species present in Florida waters generally bracketing the range of DO sensitivities seen in 

the entire complement of species used in EPA (2000). Therefore, the approach utilized by EPA 

to derive DO criteria for marine waters of the Virginian Province (EPA 2000) was used as the 

basis for the derivation of Site Specific DO Criteria that are protective of aquatic life in the 

saltwater portions of the Lower St. Johns River. While EPA’s Virginian Province methodology 

provides the basis for the proposed SSAC for DO in the LSJR, the approach was modified 

slightly to take into account Florida’s existing Class III marine criteria and existing conditions in 

the LSJR. The deviations from the EPA approach in developing the SSAC for DO in the LSJR 

are described below with a discussion regarding how the changes affect the level of protection 

afforded by the SSAC. 

Based on the DO data collected from 1996 through 2001, only 0.2% of the daily average DO 

values measured at the Acosta Bridge site were below the current 4.0 mg/L minimum 

concentration in Florida’s current marine DO criteria. Similarly, downstream at the Dames Point 

site less than approximately 2% of the daily average DO measurements were below 4.0 mg/L. 

While using the CMC (criterion minimum concentration) of 2.3 mg/L specified in the EPA 

Virginian Province for the LSJR would likely protect aquatic life from the acute effects of 

exposure to low DO levels, a CMC of 2.3 mg/L would allow minimum DO levels in the LSJR to 

be degraded from current conditions. Therefore, it is recommended that a CMC or minimum 

criterion of 4.0 mg/L be utilized for the LSJR instead of the 2.3 mg/L value recommended by 

EPA. By increasing the CMC to 4.0 mg/L, the level of protection afforded by the proposed 

SSAC would also be increased beyond that provided by the EPA recommended approach and 

is consistent with Florida’s existing DO criteria for marine waters. 

In addition, it is recommended that EPA’s recommended CCC (criterion continuous 

concentration) of 4.8 mg/L be adjusted upward to 5.0 mg/L. In deriving the CCC, EPA 

“adjusted” the total number of species (i.e., “n”) from the 11 species for which growth response 

data were available to the 22 species for which acute response data were available. 

Recalculating the CCC based on an “n” of 11, a value of approximately 5 mg/L is obtained. 

Additionally, the use of a 5.0 mg/L CCC instead of EPA’s recommended 4.8 mg/L is consistent 

with the State’s existing criteria and would provide a basis for requiring permitted discharges to 

continue to comply with 5.0 mg/L discharge limits currently in place. The use of 5.0 mg/L as the 

CCC would also afford a slightly increased level of protection compared to EPA’s recommended 

value of 4.8 mg/L. 

In the DO range between the CMC (4.0 mg/L) and the CCC (5.0 mg/L) the allowable 

duration within a portion of this range would be defined by the EPA’s recommended Final 

Recruitment Curve (FRC) (EPA 2000 as shown in Figure 3). However, EPA’s FRC plateaus at 

 92 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

approximately 4.6 mg/L leaving the effect of exposure to DO concentrations in the interval 

between 4.6 mg/L and the CCC of 5.0 mg/L difficult to interpret. Since the EPA’s FRC is based 

on the larval recruitment/survival of sensitive species, an additional component could be added 

to consider the larval growth response of sensitive species to interpret the effect of exposure to 

DO levels between the FRC and the CCC. 

The proposed SSAC for DO in the LSJR utilizes the dose-response relationship between 

DO and growth of the most sensitive species identified by EPA (EPA 2000). In the 

documentation of the derivation of the DO criteria for the Virginian Province (EPA 2000), 

Homarus americanus (American lobster) is identified as the most sensitive species to low DO 

levels. As discussed previously, since species known to inhabit Florida waters generally 

bracket the range of sensitivities to low DO levels, it is not unreasonable to use data for the 

American lobster to represent an equally sensitive species that could potentially exist in the 

LSJR for which data does not exist. The use of the response of the American lobster in 

southern waters is also consistent with EPA guidance (EPA 2000). Additionally, using the 

single most sensitive species to develop the larval growth component of the SSAC would be 

very conservative and yield a criterion that is highly protective of all aquatic life. 

As shown in Figure 4, using the data provided by EPA in the derivation of the Virginian 

Province DO criteria (EPA 2000), the lobster dose-response curve is approximated by a linear 

function: 

(equation 1) Gfr = −0.231∗[DO]+ 1.381

where Gfr is the fractional reduction in growth rate below that of controls and [DO] is the 

dissolved oxygen concentration in mg/L. Using this function to determine the degree of growth 

reduction associated with a given [DO], the impact on growth of a given duration of exposure to 

a range of concentration in DO can be estimated by another function: 

 (equation 2) Rygp = ∗ T/GT gfre

where Rygp is the fractional reduction of the year’s larval and juvenile growth potential for the 

most sensitive species, Te is the days of exposure within a specified range in concentration of 

dissolved oxygen, and Tg is the number of days within the year when larval and juvenile growth 

primarily occurs. 

If equation 1 is then substituted for Gfr in equation 2 and equation 2 is then solved for Te, the 

resulting equation becomes: 

 (equation 3)

0.231 [DO] 1.381

RT yg

e

+∗

T

∗ pg

−=

A value of 0.05 can be inserted for Rygp to specify that no more than a 5% reduction in 

growth across the larval population on an annual basis is acceptable. Using a Rygp value of 

0.05 is consistent with acceptable level of impairment used by EPA in the derivation of the 

Virginian Province DO criteria. The annual number of days in which larval and juvenile growth 

of sensitive species can be expected to occur can be estimated using growth information 

available for sensitive species indigenous to the LSJR. The available information (Vernberg and 

Piyatirattivorakul, 1998; Tagatz, 1968) indicates that significant growth is inhibited at 

temperatures below 15°C and increases markedly between 15 and 20°C. Using the mid-point 

of this range, significant growth of the sensitive species in the LSJR can be considered to occur 

 93 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

at temperatures of 17.5°C and above. Further, using the USGS monitoring data collected at the 

Acosta Bridge and Dames Point sites in the LSJR between 1996 and 2001, the annual number 

of days in which the water temperature is at or above 17.5 °C ranged from 261 to 291 with an 

average of 275 days being at or above 17.5°C. 

Inserting the values of 0.05 for Rygp and 275 for Tg into equation 3, the equation becomes: 

 (equation 4) [DO]0.231 1.381

13.7

+∗ − 5 Te =

The growth function described by equation 4 is plotted for exposure durations from 20 to 70 

days in Figure 5 along with a graphic representation of the other components (i.e., CCC, CMC, 

and FRC) of the proposed DO SSAC for the LSJR. The larval growth function intersects the 

larval population survival function (i.e., EPA’s FRC) at a DO concentration of approximately 4.6 

mg/L. This indicates that the larval population survival function would apply at DO 

concentrations between the CMC of 4.0 mg/L and 4.6 mg/L while the added growth function 

based on the lobster would apply over the DO range from 4.6 mg/L to the CCC of 5.0 mg/L. 

Utilizing a combination of the larval population survival function (EPA’s FRC) and the larval 

growth function in this manner, the proposed SSAC for the LSJR provides protection to both 

larval population recruitment/survival as well as larval growth. 

By comparing EPA’s DO criteria for the Virginian Province depicted in Figure 3 with the 

components of the proposed DO SSAC for the LSJR derived using a slightly modified 

application of EPA approach as illustrated in Figure 5, it is clear that each component of the 

proposed DO SSAC affords an equal or in most cases a greater level of protection to the 

aquatic life in the LSJR compared to EPA’s criteria for the Virginian Province. Therefore, the 

proposed SSAC is expected to provide more than adequate level of protection to all aquatic life 

in the LSJR from exposure to low DO levels. 

Derivation of the Proposed SSAC for DO in the LSJR 

In accordance with EPA recommendations for the Virginian Province (EPA 2000), the DO 

range between the CMC of 4.0 mg/L and CCC of 5.0 mg/L would be divided into intervals 

corresponding to the approximate accuracy of the instrumentation used to make the 

measurements. For the proposed LSJR SSAC, intervals from 4.0 to 4.2 mg/L; 4.2 to 4.4 mg/L; 

4.4 to 4.6 mg/L; 4.6 to 4.8 mg/L; and 4.8 to 5.0 mg/L based on the applicable portions of the 

larval population recruitment/ survival function (i.e., EPA’s FRC) and the larval growth function. 

The applicable larval population recruitment/survival function, and the larval growth function 

shown in Figure 5 can then be used to derive the acceptable exposure durations for each 

interval. Using the center point of each interval the maximum allowable cumulative duration of 

DO levels within the 4.0 to 4.2 mg/L; 4.2 to 4.4 mg/L; and 4.4 to 4.6 mg/L intervals would be 16, 

21, and 30 days, respectively, based on the final larval recruitment curve. Likewise, the 

maximum allowable cumulative duration of DO levels within the 4.6 to 4.8 mg/L and 4.8 to 5.0 

mg/L intervals would be 47 and 55 days, respectively, based on the larval growth curve. 

Since the biological effect of low DO exposure is cumulative across the DO intervals, the 

fractional exposures within each range would be summed as proposed by EPA (2000). The 

SSAC would be achieved if the sum of the fractional exposures was less than 1. Based on the 

 94 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

proposed SSAC for the LSJR, the sum of the fractional exposures between 4.0 and 5.0 mg/L 

can be expressed as: 

Max day 55

mg/L 5.0 - 4.8

between Days

Max day 47

mg/L 4.8 - 4.6

between Days

Max day 30

mg/L 4.6 - 4.4

between Days

Max day 21

mg/L 4.4 - 4.2

between Days

Max day 16

mg/L 4.2 - 4.0

between Days

Exposure

Fractional Total <

+

<

+

<

+

<

+

< ⎟ =

⎠

⎞ ⎜

⎝

⎛

where the number of days within each interval is based on the daily average DO 

concentration. 

For example, a year with the durations of DO levels for the intervals between 4.0 and 5.0 

mg/L as shown in Table 3, the Total Fractional Exposure can be expressed as: 

8960 55

12

47

9

30

7

21

4

16

1 Exposure Fractional Total =++++= .

Because the sum of the fractional exposures in this case is less than 1 (i.e., 0.896), the 

proposed SSAC would be achieved assuming the 4.0 mg/L minimum was not exceeded. 

DO Interval 

(mg/L) 

Example, 

Measured Interval 

Duration (days/year)

Maximum Interval 

Exposure Duration 

(days/year) a 

Fractional 

Interval 

Exposure b 

4.0 - <4.2 mg/L 1 16 0.063 

4.2 - <4.4 mg/L 4 21 0.190 

4.4 - <4.6 mg/L 7 30 0.233 

4.6 - <4.8 mg/L 9 47 0.191 

4.8 – <5.0 mg/L 12 55 0.218 

 Total Fractional Exposure 0.896 a

 Maximum exposure durations for intervals between 4.0 and 4.6 mg/L were determined 

from EPA Final Recruitment Curve and for intervals between 4.6 and 5.0 mg/L maximum 

exposure durations were determined from the larval growth curve (see Figure 5). 

b

 Fractional interval exposure is the measured interval duration divided by the maximum 

exposure duration for that interval. 

 95 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Final Proposed SSAC for DO in the LSJR 

From the information provided above, the proposed SSAC for DO in the LSJR would be 

comprised of two parts. The first part of the proposed SSAC is a minimum DO concentration of 

4.0 mg/L. In addition, the Total Fractional Exposure to DO levels in the 4.0 to 5.0 mg/L range 

must also be at or below 1.0 for each annual evaluation period as determined by the equation: 

Exposure Max day 16 Max day 21 Max day 30 Max day 47 Max day 55 ⎟ = + + + + ⎠ ⎜

⎝

mg/L 5.0 - 4.8

between Days

mg/L 4.8 - 4.6

between Days

mg/L 4.6 - 4.4

between Days

mg/L 4.4 - 4.2

between Days

mg/L 4.2 - 4.0

between Days

⎛ Fractional Total ⎞ < < < < <

where the number of days within each interval is based on the daily average DO 

concentration. 

Therefore, the proposed SSAC for DO in the LSJR would be a minimum concentration of 

4.0 mg/L and a Total Fractional Exposure in the range of 4.0 to 5.0 mg/L of 1.0 or less as 

determined by the equation above. The proposed SSAC would be utilized to assess the 

ambient DO status of the waters in the LSJR. It is anticipated that permitted discharges would 

continue to be required to achieve a DO concentration equal to or above the 5.0 mg/L CCC 

indicated in Figure 5. 

 96 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

 97 

Florida Department of Environmental Protection 

y = -0.2314x + 1.3

R2

 = 0.7982

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

110%

1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0

Dissolved Oxygen Concentration (mg/L)

Growth Reduction (%)

807

5.5

Figure 4. Growth response curve for the American lobster (Homarus americanus) 

exposed to various continuous low DO concentrations. Graph 

reproduced from EPA 2000. 

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

5.5

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75

Exposure Time (days)

Dissolved Oxygen (mg/L)

Larval Growth Curve

Growth (CCC) = 5.0 mg/L

Larval Population 

Recruitment (FRC)

Minimum Concentration (CMC) = 4.0 mg/L

Figure 5. Plot of the various components of the proposed SSAC for DO in the 

LSJR
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Literature Cited

CSA, Inc. 1993. Fish Assemblages Inhabiting an Oligohaline Segment of the Lower St. Johns 

River, Florida. St. Johns River Water Management District Special Publication SJ93-SP11. 

75 pp. DeMott, W.R. and F. 

Florida Marine Research Institute. 2002. Fisheries Independent Monitoring Program 2001, 

Annual Data Summary Report. Florida Marine Research Institute, St. Petersburg, Florida. 

Frydenborg R. 2005. Personal Communication. Florida Department of Enviromental 

Protection, Bureau of Laboratories, Tallahassee, FL. 

Hendrickson J, EF Lowe, D Dobberhuhl, P Sucsy, D Campbell. 2003. Characteristics of 

Accelerated Eutrophication in the Lower St. Johns River Estuary and Recommended 

Targets to Achieve Water Quality Goals for the Fulfillment of TMDL and PLRG Objectives. 

St. Johns Rivers Water Management District, Palatka, FL. 

Stephan CE, Mount DI, Hansen DJ, Gentile GH, Chapman GA, Brungs WA. 1985. Guidelines 

for deriving numerical national water quality criteria for the protection of aquatic organisms 

and their uses. National Technical Information Service Publication No.: PB85-227049. 

Tagatz, M.E., 1968. Biology of the Blue crab, Callinectes sapidus Rathburn, in the St. Johns 

River, Florida. Fishery Bullentin, 67(1):17:33. 

Thursby GB. 2003. National Saltwater Criteria for Dissolved Oxygen: Potential Addenda to 

Virginian Province Saltwater Criteria for Warmer and Colder Waters. Environmental 

Protection Agency, Office of Research and Development, Narragansett, RI. AED-03-113. 

U.S. EPA. 2000. Ambient Aquatic Life Water Quality Criteria for Dissolved Oxygen (Saltwater): 

Cape Cod to Cape Hattaras. Environmental Protection Agency, Office of Water, Washington 

D.C. PA-822-R-00-012. 

Vernberg, J. and S. Piyatirattivorakul, 1998. Effects of salinity and temperature on the 

bioenergetics of adult stages of the grass shrimp (Palaemonetes pugio Holthuis) from the 

north inlet estuary, South Carolinia. Estuarties, 21(1): 176-193. 

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Florida Department of Environmental Protection 
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Florida Department of Environmental Protection 
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100 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix M: Determination of Nitrogen and 

Phosphorus Nonpoint Loads for Urban Stormwater 

Jurisdictions 

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FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Determination of Nitrogen and Phosphorus Non-Point 

Source Loads for Urban Stormwater Jurisdictions of 

the Lower St. Johns River Basin 

John Hendrickson, Environmental Scientist VI, 

St. Johns River Water Managmement District 

Lower St. Johns River Basin Program 

Courtney Hart, GIS Analyst 

Idea Integration, Inc. 

August 2007 

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Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Determination of Nitrogen and Phosphorus Non-Point Source 

Loads for Urban Stormwater Jurisdictions of the Lower St. 

Johns River Basin 

Purpose 

• To allocate urban stormwater load reductions to responsible parties 

• To partition urban stormwater into loads emanating from old urban areas developed prior 

to the requirement of stormwater BMPs, and new urban area loads, a necessary 

distinction for establishing TMDL formula level 2 and level 3 reductions 

• To establish a relative value on which to base trading pollution reductions to other point 

and non-point entities. 

• To determine the spatial characteristics of urban area load reductions for verification of 

the revised TMDL 

Background 

This effort represents the third revision of the calculation of urban stormwater/nonpoint source 

loads for the lower St. Johns River Basin. The first iteration calculated loads only for major 

governmental entities (whole counties or municipalities with phase I or II NPDES stormwater 

permits). This calculation was later revised to distinguish MS4 areas within counties. However, 

this second analysis was incomplete, as it failed to account for urban area loads outside of 

designated MS4 areas. 

This third revision represents the most complete examination of urban stormwater loads from 

the lower St. Johns River Basin and their categorization with regard to NPDES stormwater 

permitting authority and the TMDL. Under the TMDL, allowable loadings are allocated between 

point source loads which are expressed as part of the wasteload allocation(WLA) and nonpoint 

loads which are part of the load allocations (LA). Although stormwater discharges traditionally 

are considered to be nonpoint sources of pollution, certain urban stormwater discharges legally 

are considered to be point sources since they are covered by a NPDES MS4 stormwater permit. 

These urban stormwater point sources are placed under the WLA side of the TMDL equation. 

All other loads are placed under the LA category, including natural background loads, 

atmospheric deposition, augmented nonpoint source loads that occur from agriculture, forestry, 

and urban development outside of MS4 areas. The finer-scale sub-division of loads under this 

analysis expands the number or responsible urban stormwater entities contributing to the river’s 

marine reach from eight to sixteen. Together with the freshwater reach loads that are now 

included in this analysis, there are thirty-seven entities for which urban stormwater loads and 

TMDL level 2 reductions have been identified. 

This urban stormwater load assessment also benefits from more comprehensive GIS land 

use/land cover data on which to base projected 2008 nutrient loads. In earlier calculations, 

future loads were estimated from DOT traffic analysis zone population 

103 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Table 1. Urban Stormwater Jurisdictions and Areas for the Marine and Freshwater 

Contributing Basins of the LSJR 

 Jurisdiction 

WLA 

LA 

Total Area 

(Acres) 

Marine Reach Contributing Area 

Duval County Marine X 377,458

Clay Marine UA X 31,421

St. Johns County Marine UA X 13,841

Jacksonville Beach X 4,652

NAS Jacksonville X 3,843

Mayport NS X 2,822

Orange Park X 2,308

Marine Reach WLA Sub-total 436,345

Clay Marine Non-UA X 191,873

Camp Blanding X 54,929

St. Johns County Marine Non-UA X 33,334

Penney Farms X 894

 Marine Reach LA Subtotal 281,029

Freshwater Reach Contributing Area 

Green Cove Springs X 3,848

Clay County Fresh UA X 1,940

Freshwater Reach WLA Sub-total 5,788

Putnam County Fresh Non-UA X 217,472

St Johns County Fresh Non-UA X 178,548

Clay County Fresh Non-UA X 54,179

Flagler County Fresh Non-UA X 4,759

Palatka X 4,447

Welaka X 425

Hastings X 421

Pomona Park X 219

 Freshwater Reach LA Sub-total 460,470

1 UA = Urbanized Area based on 2000 Census data for NPDES Phase II applicability

projections, which were then converted by a regression model to urbanized area. Due to the 

recent availability of 2004 land use/land cover data, this analysis forecasts 2008 urban area 

through a regression model utilizing four land cover data sets from 1989 through 2004. 

104 

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105 

Florida Department of Environmental Protection 

Determination of NPDES MS4 Status and 1984 and 2008 Urban Areas 

Based on guidance provided by staff at FDEP regarding the determination of responsibilities for 

urban stormwater under the NPDES program, a GIS coverage was created by combining the 

boundaries of governmental entities (counties, municipalities, and military installations), 

established MS4 boundaries, and 2000 census urbanized areas (areas identified with urban 

stormwater permit requirements under phase II). The resulting coverage relegated the entire 

area of the LSJR basin into one of 37 mutually-exclusive areas that were NPDES Phase I, 

NPDES Phase II, or non-NPDES stormwater responsibility. A number of these areas were then 

re-combined based upon guidance from MS4 permit holders. Most notable among these 

subsumed areas was the placement of Cecil Field and the Mayport Fuel Depot into the Duval 

MS4, the combining of the St. Johns County Julington Creek Plantation and Ponte Vedra into 

one St. Johns UA category, and the placement of the East Palatka area under the Putnam 

County jurisdiction. The final list contained 21 areas (Table 1; Figure 1). This report does not 

address the individual entities adding nutrient load to the Crescent Lake Basin, and this 

contributing watershed is considered to have a single allocation. Also, karst areas within the 

LSJR basin in eastern Alachua county and western Clay county with no surface water 

connections to the St. Johns River are excluded from the allocation process. 

Successive years of land use/land cover data were overlain on these 37 areas to examine 

growth trends for the purpose of hindcasting and forecasting the 1984 urban areas (areas 

presumed to have been developed without stormwater runoff BMPs) and the 2008 urban area 

(starting point for load allocations). Figure 2 provides an example of how this calculation was 

performed for the Jacksonville Phase I area. The calculated 1984 and 2008 urbanized areas 

within each of the jurisdictional entities are listed in Table 2. Urban areas were defined in the 

land use/land cover data as the sum of low, medium and high density residential, low and high 

intensity commercial, and industrial classes. 

 

Jacksonville and Beaches

y = 1.9782x - 3801.9

R2 = 0.9989

120

130

140

150

160

170

180

1980

1985

1990

1995

2000

2005

2010

Urban Area, Thousands of Acres

1984 area = 

122,848 ac.

2008 area = 

170,325 ac. Figure 2. Example of 

urban area load 

extrapolation to 1984 and 

2008 for the Jacksonville 

and Beaches MS4 area. 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

106 

Florida Department of Environmental Protection 

Figure 1. Urban Stormwater Jurisdictions Contributing to the Marine Reach of the Lower StRiver 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure 1. Urban Stormwater Jurisdictions Contributing to the Freshwater Reach of the LoRiver 

107 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

108 

Florida Department of Environmental Protection Table 2. Estimated 1984 and 2008 Urbanized Areas within Urban Stormwater Entities 

Jurisdiction 

WLA 

LA 

Urban Areas, acres1 Comme

Marine Reach 1984 1989 1994 1999 2004 2008 

Duval County Marine X 125,895 136099 144622 154536 165417 173,023 8.0088*

Clay Marine UA X 15,001 16375 19371 21253 22138 24,203 155.22x 

St. Johns County Marine UA X 4,219 5338 5827 7084 8617 9,445 

4 22.281

East); 7(SJ Wes

Jacksonville Beach X 2,107 2265 2390 2610 2703 2,844 12.443x 

NAS Jacksonville X 2,475 2476 2311 2367 2482 2,482 No clea

Mayport NS X 1,434 1434 1313 1305 1387 1,387 No clea

Orange Park X 1,936 1937 1954 2011 2004 2,004 No clea

Clay Marine Non-UA X 16,860 16860 16780 17823 20232 21,395 139.73x 

Camp Blanding X 3,022 3022 2404 2407 2674 2,674 No clea

St. Johns Co. Marine Non-UA X 1,112 1470 1981 2051 2697 2,912 30.375x 

Penney Farms X 185 202 195 228 228 228 No clea

Freshwater Reach

Green Cove Springs X 2,188 2188 2247 1965 2041 2,041 No clea

Clay County Fresh UA X 1,152 1152 1102 1121 1098 1,098 No clea

Putnam County Fresh Non-UA X 20,764 20213 23466 24319 25925 27,603 146.28x 

St Johns County Fresh Non-UA X 4,700 8380 8832 14670 16237 18,817 238.13x 

Clay County Fresh Non-UA X 2,466 2466 3540 3446 3476 3,476 No clea

Flagler County Fresh Non-UA X 3 3 2 3 6 6 No clea

Palatka X 3,169 3169 3044 3009 3050 3,050 No clea

Welaka X 384 327 311 306 197 195 -3.1981

Hastings X 229 229 245 239 234 234 No clea

Pomona Park X 65 65 79 79 29 29 No clea

1Urban areas 1989 - 2004 from GIS Land Use coverages; 1984 and 2008 predicted. 2Regression equations based on areas in hectares; x=year 3If no clear growth trend, 1989 Urban Area =1984; 2004 Urban area = 2008 4Growth flat until 95-99; linear regression under-predicts 1984 and 2008. Trend determined from 1995-2004. 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Estimation of Representative Nutrient Concentrations for Urban 

Areas 

The underlying concepts embodied in the non-point source watershed modeling for the 

TMDL were employed to estimate urban area stormwater loads,. In this model, nutrient 

load in runoff for an area is calculated as the product of separately determined estimates 

of concentration and runoff volume. The model relies upon the premise that nutrient 

concentrations and runoff volume tend to be similar for characteristic land development 

types, owing to the fact that these land development types and the ensuing activities 

within them have similar nutrient-generating aspects. These land development types are 

derived from the Florida Land Use Land Cover classification system, with the lowest 

level urban delineations in this data layer aggregated into six super-groups of land use 

(low density residential, medium density residential, high density residential, low intensity 

commercial, high intensity commercial, and industrial), represented by the level II land 

uses of Figure 3. Because there are significant climactic, physiographic and 

developmental (mostly infrastructure related) regional aspects to the propensity for 

nutrient export in runoff from urban lands, regional data should be used to characterize 

typical land use-water quality. Harper (1994) has compiled data for studies conducted in 

Florida, to produce regionally relevant water quality statistics for these land uses. 

The land use water quality values used for the LSJR TMDL are fundamentally different 

than the Harper (1994) in their derivation. While the Harper data are compiled from 

nitrogen and phosphorus concentrations measured in runoff from small catchments of 

one predominant land development type (typically tens of acres in size), the LSJR TMDL 

watershed model values were derived from water quality monitoring data from 30 wellsampled tributaries draining large watersheds (tens to hundreds of square miles) in the 

LSJR basin. Specific land use water quality concentrations were calculated with multiple 

regressions relating seasonal flow-weighted concentrations to the fractions of major 

(level I; Figure 3) watershed land use. In watersheds where only urban development 

was present, TN and TP coefficients were also determined by extrapolating the fraction 

of developed area – nutrient concentration regressions to the point of 100 percent 

watershed land cover, as shown in the example of Figure 5. The resulting LSJR 

concentrations are lower that the Harper (1994) values (Table 3; Figure 4), presumably 

because sedimentation, denitrification and assimilation by primary and secondary 

producers reduces nutrients from their point of mobilization. The LSJR watershed 

model coefficients were adjusted in this manner to provide the most accurate values of 

watershed load to the river water quality model, as actual measured data is generally 

preferred over unsubstantiated literature values when such accuracy is desired 

(Donigian and Huber, 1991). For urban land use as a whole, the LSJR nitrogen 

concentrations tend to be 67 percent of the Harper literature data, while phosphorus 

values are similar (95 percent). The runoff coefficient (RC) values, the fraction of 

incident rainfall that ultimately ends up in streamflow at a broad temporal scale, tend to 

be half of the Harper literature values. The departure in RC arises from the very low 

value for low density residential in the LSJR TMDL model, which was assigned to reflect 

114 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure 3. Hierarchy of Land Use Classifications Used in the LSJR TMDL Non-point Source Nutrient L

Top level land use categories are referred to as “Level I”; Mid-level categories are referred Bottom boxes of the tree identify the Florida Land Use Land Classification Codes aggregaLevel II categories. 

Agriculture Forest Open Land Urban Water 

24002410242024302431243224502500

2130220022102230

214021432150216021802100

26002610

211023102320251025202540

Silviculture

Forest

Nurseries

Field Crops

Fallow

Animal Production

Groves/woodland Pastures

44004430

1910411041204130420042104280434043704410

Vegetated Successional

Mining

Bare Land

Medium Density Residential

Low Density Residential

Industrial

Low Intensity Commercial

High Intensity Commercial

Saltwater

Freshwater

16501670192019302120224031003200330074108320

16001610161116121613162016301632163316401660

1810190071007200740074207430

1480170017301750180018201850186018908110833083408350

12001290

110011801190

151015201523153015401550156015621590

140014601490183018401870812081308140815081608180820082108310819081918300

54005430

5100520052505300550056008360

High Density Residential

13001390

115 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

116 

Florida Department of Environmental Protection 

Table 3. Event Mean Concentrations of Total N and P in Runoff for Florida Studies on Small CHomogeneous Land Use, and Values derived by Regression from Large Watershed MonitorinLSJR Basin. (*)RC values reflect rural homestead-level development, and were not used the RCs for new development. 

Source Variable 

Low Density 

Residential 

Med. Density 

Residential 

High Density 

Residential 

Low Intensity 

Commercial

High In

Comme

Typical Florida Values, Small 

Catchment of Homogeneous 

Land Use 

Harper, 1994 

N 1.77 2.29 2.42 1.18 2.83 

P 0.177 0.300 0.490 0.150 0.430 

RC Avg. 

Yr 0.268 0.373 0.675 0.837 0.887 

LSJR TMDL Values, Based on 

Whole Watershed Land Use 

Hendrickson and 

Konwinski, 1998 

N 0.80 1.50 1.83 1.20 1.83 

P 0.080 0.300 0.443 0.240 0.443 

RC Avg. 

Yr. 0.123* 0.381 0.406 0.381 0.417 

RC Dry 

Yr. 0.090* 0.278 0.296 0.278 0.305 

Nitrogen

y = 0.6744x

0.51.01.52.02.5

0.5 1.5 2.5

Harper N, mg/L

LSJR N, mg/L

Phosphorus

y = 0.9439x

0.00.10.20.30.40.5

0.0 0.2 0.4 0.6

Harper P, mg/L

LSJR P, mg/L

Runoff Coeffici

0.00.10.20.30.40.5

0.0 0.5 

Harpe

LSJR RC

Figure 4. Comparison of LSJR TMDL and Small Catchment, Homogeneous Land Use N and P ConceRunoff 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Figure 5. Comparison of Old Urban and New Urban (Post 1984 with Environmental 

Resource Permit Development Practices) Nitrogen and Phosphorus Concentrations in 

Runoff

T. Bioavailable N

y = 1.6936x1.2933

R2 = 0.8458

y = 0.7674x

R2

 = 0.6936

0

0.5

1

1.5

2

2.5

0.0 0.2 0.4 0.6 0.8 1.0

Fraction of Developed Watershed Area

TBN, mg/L

Old Urban

New Urban

TP

y = 0.391x1.6076

R2 = 0.6971

y = 0.0931x

R2

 = 0.6958

0

0.07

0.14

0.21

0.28

0.35

0.42

0.0 0.2 0.4 0.6 0.8 1.0

Fraction of Developed Watershed Area

TP, mg/L

Old Urban

New Urban

very low development density typical of rural homesteads, and does not reflect the development 

density assigned to low density residential in the LSJR basin. Due to this large departure from 

the Harper literature values, this RC value was not used in load calculations for new 

development. 

 

The LSJR TMDL typical urban area nutrient concentrations are considered to be representative 

of “old” urban because the data from which they are derived were collected in the early to mid 

1990’s from streams draining areas developed prior to 1984, located in the densely developed 

areas of Jacksonville and northern Clay County. There are several noteworthy characteristics 

of development subsequent to 1984 that reduce the nutrient concentrations in runoff. The 

addition of stormwater treatment requirements, impervious area runoff retention, wetland 

protection, lower overall development density, and the use of sanitary sewer collection instead 

of septic tanks all are believed to play a role in the lower N and P concentrations observed in 

post-1984 development. While it would have been possible to model, in a more mechanistic 

way, typical N and P concentrations representative of newer development by applying literature 

values on the typical efficiency of stormwater treatment practices, it was felt that this would 

under-represent the total nutrient load reduction that occurs from the “treatment train” of the 

additional characteristics listed above. This approach would also not be able to characterize the 

nature of changes that current stormwater treatment has on the lability of organic nitrogen, a 

necessary piece of information in subsequent river water quality modeling (a significant portion 

of organic nitrogen in natural blackwater stream runoff is refractory, or not readily assimilable by 

algae in time relevant time frames). For these reasons, monitoring from watersheds of only new 

development was again relied upon to extrapolate to 100 percent model coefficients. Presently, 

there is a limited amount of data from watersheds dominated by new development, but several 

sub-watersheds within the large developments of regional impact of Eagle Harbor and Julington 

Creek Plantation have sufficient data to make preliminary estimates. Using the procedure of 

extrapolating the developed area of these newly developed residential and commercial 

developments to 100 percent (Figure 5), a “new” development total bioavailable N (TBN) 

117 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

concentration of around 0.93 mg/L, and TP concentration of around 0.13 mg/L, can be 

calculated. 

Due to the increased amount of impervious surface area in urbanized watersheds, a greater 

amount of rainfall is directed to runoff, thus increasing the nutrient load. The mean of urban 

land use RC values used in the TMDL modeling (again representative of older urban areas at a 

watershed scale) ranged from 0.123 to 0.417, with an average of 0.393 (low density residential 

omitted). This RC value represents the ratio of runoff to rainfall volume for the watershed scale, 

long-term average rainfall condition, but in a dry year, the propensity for a rainfall event to 

generate runoff is reduced, due to soil and vegetation moisture deficits. To account for this in 

the stormwater source load estimate, the RC was varied based upon a calibration to the ratio of 

the particular season’s rainfall to the long-term rain for that season and for previous seasons, 

with a factor referred to as the long-term rain ratio. Thus, for the extreme 1999 dry-year case, 

the urban RC ranged from 0.09 to 0.305, with and overall mean value of 0.287 (low density 

residential omitted). Insufficient information exists to characterize an RC representative of new 

urban development at the watershed scale, so this value was estimated by multiplying a 

hydrologic efficiency of 0.8 for stormwater wet ponds (hydrologic efficiency being the ratio of wet 

pond exiting volume to that of the total incoming volume; this value is assumed less than 1, as 

wet pond water volume is lost to evapotranspiration and shallow ground water infiltration) times 

the aggregate urban land runoff coefficients for average or dry years. 

N and P removal Efficiencies for Calculation of TMDL Level 2 

Reductions 

Nutrient pollutant removal achieved by retrofitted best management practices is dependent 

upon the particular nutrient form, the treatment system, and the design considerations of the 

particular system. Even for specific system types, removal efficiencies are highly variable. 

Because wet detention if the most commonly applied system for urban stormwater retrofit, 

published efficiencies for this type of system were used. CDM (2002) provides a range for 

treatment efficiency for TP of 40 to 50 percent, for TKN of between 20 to 30 percent, and for 

NOX of between 30 to 40 percent. Harper (2003) provides equations on the efficiency of wet 

detention systems based upon residence time. For a 2-week retention time (typical wet pond 

design target), removal efficiencies were calculated as: 

Total N: 8.4126*[Ln(Time, Days)] + 27.25 = 49% 

Total P: 8.0847*[Ln(Time, days)] + 44.583 = 66% 

Winer (2000) lists nutrient pollution removal efficiencies for stormwater wet ponds of 51% for 

TP, 66% for soluble P, 33% for TN and 43% for NOX. For calculation of removal efficiencies 

commensurate with level 2 stormwater retrofit, conservative, low to mid range values have been 

selected of 30% for TN, and 50% for TP. 

Estimation of Urban Area Loads 

The Florida Watershed Restoration Act of 1999 directed the Department of Environmental 

Protection to convene a committee of experts to advise the legislature on the approach to 

allocating sustainable pollutant loads under the TMDL process. This Allocation Technical 

Advisory Committee (FDEP, 2001) recommended a stepped process for the reduction of 

pollutant loads to water bodies. A central concept to this allocation process was that while point 

118 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

sources of pollution throughout the State had instituted accepted technologies to reduce 

pollutant load, and were operating under permit, most non-point sources of pollution continued 

unabated. It was the consensus of the committee that reductions in pollutant load should begin 

first with uncontrolled (non-treated) urban stormwater runoff, prior to the requirement of higher 

treatment levels from point sources of pollution. Urban stormwater sources were to first institute 

stormwater management for 45 percent of uncontrolled areas (referred to as level 1), and if this 

was insufficient, expand area of treatment to 90 percent of uncontrolled areas (level 2). If the 

level 2 urban stormwater control was insufficient to achieve the TMDL, then point and nonpoint 

sources shared equal burdens to reduce the remaining excess load. 

To apply this allocation guidance to urban stormwater sources of nutrient pollution in the LSJR 

basin, N and P loads were estimated for: 

1. urban areas without stormwater treatment, presumed to be all urban development that 

occurred prior to the enactment of F.A.C. 40C-4 (Management and Storage of Surface 

Waters), and later, the general Environmental Resource Permit (F.A.C. 40C-42), as this 

load would need to be assessed level 1 or level 2 reductions; and 

2. urban development with stormwater BMPs, presumed to be new development, or that 

development that has occurred since 1984, forecast to 2008. 

To calculate the untreated urban area loads, the 1989 land use data was aggregated into the six 

urban subclasses for which typical water quality nutrient concentrations have been determined 

(Table 2), and loads determined as: 

(NCi)∗(RCi)∗(RAINj)∗(AREAk) 

Where: 

NCi = the nutrient concentration for land use i

RCi = the runoff coefficient for land use i

RAINj = the rainfall amount for the year j, the average annual condition for the 

 freshwater reach, or the dry year total for the marine reach, and 

AREAk = the area of urban land use i for MS4 area k. 

The urban N and P loads derived from the 1989 land use data were multiplied by the ratio of the 

1984 urban area:1989 urban area ratio, with the 1984 urban area predicted by the urban area 

change over time regressions of Table 2, to provide an estimate of 1984 urban area load. 

To estimate the N and P load associated with urban development subsequent to 1984, the 

formula above was again applied, with the overall urban concentration values of 0.93 mg/L N 

and 0.13 mg/L P used to represent the aggregate of all urban development categories. Runoff 

volume was estimated with mean RC values of 0.387 for the average year rain condition, or 

0.293 to reflect the dry year condition, with each of these values multiplied by 0.8 to reflect the 

reduction in runoff by stormwater pond hydraulic efficiency. These single values were used in 

this load calculation, rather than individual land use category coefficients, as data are not 

currently available to calculate these watershed scale “new development” rates. 

Tables 4 through 7 list the calculated old urban development loads, new urban development 

loads, total loads and level 2 reductions for both the marine reach and freshwater reach 

contributing watersheds of the LSJR basin. Old urban area loads are calculated as described 

above and summed for each of the individual loads of the six urban land development 

119 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

categories, while new urban area loads are determined from the single composite nitrogen and 

phosphorus concentration and RC values described above. Level 2 load reductions are 

determined on the old urban area load only, using the 30 percent reduction for nitrogen and 50 

percent reduction for phosphorus described above. 

Other Considerations 

• It should be noted that these calculations concentrate only on the estimation of nitrogen 

and phosphorus stormwater loads for urban areas, on the distinction of old urban areas 

that would indicate candidate loads for level 2 reductions, and the changes in this load 

representative of average rainfall years and the 1999 dry year. Additional TMDL level 3 

load reductions are levied upon these urban stormwater jurisdictions through a separate 

calculation that incorporates point source loads. 

• The old urban area loads calculated here should theoretically be greater than the actual 

loads, as most of these jurisdictions have instituted some levels stormwater retrofit in 

their older urban areas, extension of sanitary sewer service, street sweeping, etc., that 

would act to reduce the loads. Credit can be claimed for nutrient load reduction from 

such projects and activities. 

• While stormwater entities have been delineated for the Crescent Lake Basin, the 

calculations have not been presented on their old and new development loads and 

reductions, as at this point in the TMDL allocation process the basin is being provided 

with a single allocation. 

Table 4. Calculated Average Rainfall Urban Stormwater Source Nitrogen Loads for 

Jurisdictions of the Marine Reach of the Lower St. Johns River, MT/yr 

Marine Reach Jurisdiction 

WLA 

LA 

1984/1989 

Urban 

Area Ratio

Old (1984) 

Urban Area 

TN Load, 

(MT/yr) 

New Urban 

Area TN 

Load, 1984-

2008, (MT/yr)

Total 2008 

Projected 

TN Load, 

(MT/yr) 

Level 2 

Reduction (90% 

Old Urban 

Retrofit, MT/yr)

Jacksonville, FDOT and 

Beaches X 0.93 346.5 74.9 421.5 93.6 

Clay Co. Marine w/in UA X 0.89 28.2 14.4 42.7 7.6 

St. Johns Co. X 0.80 10.4 8.2 18.7 2.8 

Jacksonville Beach X 0.94 7.3 1.1 8.4 2.0 

NAS Jacksonville X 1.00 8.0 0.0 8.1 2.2 

Orange Park X 1.00 5.7 0.1 5.8 1.6 

Mayport NS X 1.00 4.7 0.0 4.7 1.26 

Clay Co. Marine non-UA X 0.95 15.3 7.2 22.5 4.14 

Camp Blanding X 1.00 4.4 3.4 7.9 1.2 

SJC remaining marine X 0.80 1.8 2.2 4.0 0.5 

Penney Farms X 0.94 0.2 0.1 0.3 0.1 

TOTAL 432.5 111.6 544.6 117 

120 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Table 5. Calculated Dry-Year (1999) Urban Stormwater Source Nitrogen Loads for 

Jurisdictions of the Marine Reach of the Lower St. Johns River, MT/yr 

Marine Reach Jurisdiction 

WLA 

LA 

1984/1989 

Urban Area 

Ratio 

Old (1984) 

Urban Area 

TN Load, 

(MT/yr) 

New Urban 

Area TN 

Load, 1984-

2008, 

(MT/yr) 

Total 2008 

Projected 

TN Load, 

(MT/yr) 

Level 2 

Reduction (90% 

Old Urban 

Retrofit, MT/yr)

Jacksonville, FDOT and 

Beaches X 0.93 206.3 44.4 247.4 55.7 

Clay Co. Marine w/in UA X 0.89 16.7 8.5 25.2 4.5 

St. Johns Co. X 0.80 5.9 4.9 10.5 1.6 

Jacksonville Beach X 0.94 4.3 0.7 5.0 1.2 

NAS Jacksonville X 1.00 4.8 0.0 4.8 1.3 

Orange Park X 1.00 3.4 0.1 3.5 0.9 

Mayport NS X 1.00 2.8 0.0 2.8 0.7 

Clay Co. Marine non-UA X 0.95 8.4 4.2 12.1 2.3 

Camp Blanding X 1.00 2.6 2.0 4.7 0.7 

SJC remaining marine X 0.80 1.1 1.3 2.4 0.3 

Penney Farms X 0.94 0.1 0.0 0.2 0.0 

TOTAL 256.4 66.1 318.6 69.2 256.4 

Table 6. Calculated Average Rainfall Urban Stormwater Source Nitrogen Loads for 

Jurisdictions of the Freshwater Reach of the Lower St. Johns River, MT/yr 

NITROGEN 

Freshwater Reach 

Jurisdiction 

WLA 

LA 

1984/1989 

Urban Area 

Ratio 

Old (1984) 

Urban Area 

TN Load, 

(MT/yr) 

New Urban 

Area TN 

Load, 1984-

2008, (MT/yr)

Total 2008 

Projected 

TN Load, 

(MT/yr) 

Level 2 

Reduction (90% 

Old Urban 

Retrofit, MT/yr)

Green Cove Springs X 1.00 6.96 0.00 6.96 1.88 

Clay Co. Fresh w/in UA X 1.00 2.77 0.00 2.77 0.75 

Putnam Co. non-UA X 1.03 32.78 10.84 43.62 8.85 

St. Johns Co. non-UA X 0.56 4.96 22.25 27.21 1.34 

Palatka X 1.00 9.68 0.00 9.68 2.61 

Clay Co. Fresh non-UA X 1.00 3.99 1.60 5.59 1.08 

Welaka X 1.17 1.17 0.00 1.17 0.32 

Hastings X 1.00 0.62 0.01 0.62 0.17 

Alachua Co. non-UA X 1.00 0.10 0.54 0.64 0.03 

Pomona Park X 1.00 0.11 0.00 0.11 0.03 

Flagler Co. Non-UA X 1.00 0.00 0.01 0.01 0.00 

121 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Table 7. Calculated Average Rainfall Urban Stormwater Source Phosphorus Loads for 

Jurisdictions of the Freshwater Reach of the Lower St. Johns River, MT/yr 

PHOSPHORUS 

Freshwater Reach 

Jurisdiction 

WLA 

LA 

1984/1989 

Urban 

Area Ratio

Old (1984) 

Urban Area 

TP Load, 

(MT/yr) 

New Urban 

Area TP 

Load, 1984-

2008, (MT/yr)

Total 2008 

Projected 

TP Load, 

(MT/yr) 

Level 2 

Reduction (90% 

Old Urban 

Retrofit, MT/yr)

Green Cove Springs X 1.00 1.10 0.00 1.10 0.49 

Clay Co. Fresh w/in UA X 1.00 0.40 0.00 0.40 0.18 

Putnam Co. non-UA X 1.03 4.47 1.52 6.00 2.01 

St. Johns Co. non-UA X 0.56 1.51 0.00 1.51 0.68 

Palatka X 1.00 0.62 3.11 3.73 0.28 

Clay Co. Fresh non-UA X 1.00 0.54 0.22 0.77 0.24 

Welaka X 1.17 0.17 0.00 0.17 0.08 

Hastings X 1.00 0.09 0.00 0.09 0.04 

Alachua Co. non-UA X 1.00 0.02 0.00 0.02 0.01 

Pomona Park X 1.00 0.01 0.08 0.08 0.00 

Flagler Co. Non-UA X 1.00 0.00 0.00 0.00 0.00 

122 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Literature Cited 

CDM, 2002. Literature Review of Stormwater Best Management Practices. Camp, Dresser and 

McKee. St. Johns River Water Management District Technical Memorandum. 

Donigan, A.S. and W.C. Huber. 1991. Modeling of nonpoint source watewr quality in urban and 

non-urban areas. EPA/600/3-91/039. U.S. Environmental Protection Agency, Office of 

research and Development, Washington, D.C. 

FDEP, 2001. A Report to the Governor and Legislature on the Allocation of Total Maximum 

Daily Loads in Florida. FDEP Bureau of Watershed Management, Tallahasee, FL. 

Harper, H.H. 2003. Evaluation of Alternative Stormwater Regulations for Southwest Florida. 

Report submitted to Water Enhancement and Restoration Coalition, Inc. Prepared by 

Environmental Research and Design, Orlando, FL 

Harper, H.H. 1994. Stormwater loading rate parameters for central and south Florida. 

Environmental Research and Design, Inc. Orlando, FL. 

Hendrickson, J.C. and J. Konwinski. 1998. Seasonal Nutrient Import-Export Budgets for the 

Lower St. Johns River, Florida. Report prepared for the Florida Department of Environmental 

Protection under Contract WM598. 109 PP> 

Winer, R. 2000. National Pollutant Removal Performance Database for Stormwater Treatment 

Practices 2nd Ed. Center for Watershed Protection, Endicott City, MD. prepared for U.S. EPA 

Office of Science and Technology. 

123 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix N: Comparisons Between Existing 1999 

Simulation and TMDL Simulation for Marine WBID DO 

and Freshwater Chlorophyll 

Daily average DO and total fractional exposure under the current conditions simulation 

for 1999 in WBIDs 2213A – 2213D 

WBID Minimum Daily Mean DO WBID Mean SSAC Dose 

YEAR A B C D A B C D 

1999 4.13 4.06 4.26 4.39 2.62 2.00 1.59 0.56 

Daily average DO and total fractional exposure under the TMDL simulation for 1999 in 

WBIDS 2213A – 2213D 

WBID Minimum Daily Mean DO WBID Mean SSAC Dose 

YEAR A B C D A B C D 

1999 4.52 4.53 4.66 4.8 0.99 0.87 0.42 0.06 

124 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

125 

Florida Department of Environmental Protection 

MODEL DAILY DO VALUES (WBID A)

3

4

5

6

7

8

9

12/1/1998

1/1/19992/1/19993/1/19994/1/19995/1/19996/1/19997/1/19998/1/19999/1/1999

10/1/199911/1/1999

DATE

DISSOLVED OXYGEN 

(MG/L)

TMDL CURRENT

MODEL DAILY DO VALUES (WBID B)

3

4

5

6

7

8

9

12/1/1998

1/1/19992/1/19993/1/19994/1/19995/1/19996/1/19997/1/19998/1/19999/1/1999

10/1/199911/1/1999

DATE

DISSOLVED OXYGEN 

(MG/L)

TMDL CURRENT

MODEL DAILY DO VALUES (WBID C)

3

4

5

6

7

8

9

12/1/1998

1/1/19992/1/19993/1/19994/1/19995/1/19996/1/19997/1/19998/1/19999/1/1999

10/1/199911/1/1999

DATE

DISSOLVED OXYGEN 

(MG/L)

TMDL CURRENT

MODEL DAILY DO VALUES (WBID D)

3

4

5

6

7

8

9

10

12/1/1998

1/1/19992/1/19993/1/19994/1/19995/1/19996/1/19997/1/19998/1/19999/1/1999

10/1/199911/1/1999

DATE

DISSOLVED OXYGEN 

(MG/L)

TMDL CURRENT

MODEL DAILY DO VALUES (WBID E)

4

5

6

7

8

9

10

11

12/1/1998

1/1/19992/1/19993/1/19994/1/19995/1/19996/1/19997/1/19998/1/19999/1/1999

10/1/199911/1/1999

DATE

DISSOLVED OXYGEN 

(MG/L)

TMDL CURRENT

MODEL DAILY DO VALUES (WBID F)

4

5

6

7

8

9

10

11

12/1/1998

1/1/19992/1/19993/1/19994/1/19995/1/19996/1/19997/1/19998/1/19999/1/1999

10/1/199911/1/1999

DATE

DISSOLVED OXYGEN 

(MG/L)

TMDL CURRENT
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

KEY STATISTICS FOR SELECTED FRESHWATER SITES FROM 1999 MODEL YEAR SIMULA

Statistic Hibernia Picolata Racy Pt. Federal Pt. 

Existing TMDL Existing TMDL Existing TMDL Existing TMDL 

Chla min (ug/L) 0.92 0.84 2.64 2.3 11.4 9.74 11.06 10.6 Chla max (ug/L) 49.82 28.46 61.06 33.4 89.24 58.6 88.84 61.42 Chla median (ug/L) 11.16 8.01 16.88 11.73 25.68 20.05 28.14 21.92 # days Chla > 40 ug/L 16 0 20 0 109 55 122 77 % of year Chla > 40 ug/L 4.4 0 5.5 0 29.9 15.1 33.4 21.1 # Consecutive days Chla > 40 ug/L 10 0 13 0 39 21 53 43 

126 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

CUMULATIVE FREQUENCY DAILY CHLA PLOTS FOR 1999 BASED ON MODEL 

SIMULATION OF THE EXISTING AND TMDL SCENARIOS 

HIBERNIA CHLA FREQUENCY

0

20

40

60

80

100

0 5 10 15 20 25 30 35 40 45 50 55 60

DAILY CHLA (UG/L)

PERCENT

TMDL existing

PICOLATO CHLA FREQUENCY

0

20

40

60

80

100

0 10 20 30 40 50 60 70

DAILY CHLA (UG/L)

PERCENT

TMDLl existing

WATSON CHLA FREQUENCY

0

20

40

60

80

100

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70

DAILY CHLA (UG/L)

PERCENT

TMDL existing

RACYPT CHLA FREQUENCY

0

20

40

60

80

100

0 20 40 60 80 100

DAILY CHLA (UG/L)

PERCENT

TMDL existing

FEDERAL PT CHLA FREQUENCY

0

20

40

60

80

100

0 5 10 15 20 25 30 35 40 45 50 55 60 65 70

DAILY CHLA (UG/L)

PERCENT

TMDL existing

PALATKA CHLA FREQUENCY

0

20

40

60

80

100

0 20 40 60 80 100

DAILY CHLA (UG/L)

PERCENT

TMDL existing

127 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

CUMULATIVE FREQUENCY PLOTS FOR DAILY CHLA MAXIMUM FROM THE 1999 

TMDL SIMULATION 

FULTON

0.000.250.500.751.001.251.501.752.002.252.502.753.003.253.503.754.004.254.504.755.00

Max daily Chla (ug/l)

0.00

0.05

0.10

0.15

0.20

0.25

0.30

0.35

0.40

0.45

0.50

0.55

0.60

0.65

0.70

0.75

0.80

0.85

0.90

0.95

1.00

FR

A

C

T

OI N of D

A

T

A

TALLYRAND

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128 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Appendix O: Responsiveness Summary to Public 

Comments on Draft TMDL following March 2008 

Public Meeting 

March 05, 2008 

Darryl Joiner 

Environmental Manager 

Water Quality Standards & 

Special Projects Program 

Florida Department of 

Environmental Protection 

2600 Blair Stone Road, MS 3560 

Tallahassee, FL 32399-2400 

RE: Establishment of site specific alternative criteria for dissolved oxygen in the 

marine portions of the lower St. Johns River and its tributaries. 

Dear Mr. Joyner, 

The following comments on the establishment of site specific alternative criteria (SSAC) 

for dissolved oxygen (DO) in the marine portions of the lower St. Johns River (LSJR or 

River) and its tributaries, proposed by the Florida Department of Environmental 

Protection (FDEP) are submitted by the St. Johns Riverkeeper. 

You may recognize these comments. They’re basically the same comments we 

submitted to the Department over two years ago. Evidently, the DEP didn’t consider 

their merits then, and I don’t expect more scrutiny now. I do, however, believe it is 

important to state that we oppose the entire SSAC travesty, charade, actually. This 

correspondence will establish standing as we, and others, continue to explore 

appropriate legal venues in which to continue our legal challenges to the SSAC. 

We oppose the establishment of the proposed DO SSAC for the LSJR. Based upon the 

data we received at the recent SSAC public hearing, the proposed TMDL utilizing the 

SSAC will allow the discharge of an additional 1 million lbs. of nitrogen per year into the 

lower St. Johns River beyond what is currently allowed. 

The FDEP has failed both scientifically, and administratively, to make the case that the 

proposed SSAC for the LSJR is warranted or indeed, even appropriate. 

Our opposition to the SSCA is based upon the following reasons: 

1. IT IS INAPPROPRIATE TO DEVELOP THE LSJR DO SSAC USING THE 

ENVIRONMENTAL PROTECTION AGENCY’S (EPA) APPROACH FOR 

THE VIRGINIAN PROVINCE (VP). 

129 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Our opposition to the methodology FDEP employed to develop the draft SSAC should 

come as no surprise to the department. Riverkeeper and Clean Water Network 

questioned the use of the VP guidance in our comments we submitted for the 

September 30, 2003, Rule Adoption Hearing in Tallahassee for the FDEP nutrient 

TMDL. (Jerry Brooks was the hearing officer.) At that time we stated, “We question the 

applicability of this document to the lower St. Johns River ecosystem. If fact, we reject 

the comparison.” Today, 28 months later, we have not changed our opinion. 

The FDEP expects the public to buy into their theory that the LSJR is exactly like the VP, 

an area bordered by Cape Cod on the north and Cape Hatteras on the south. Using that 

hypothesis as its basis, the DEP has used the report entitled, Ambient Aquatic Life 

Water Quality Criteria for Dissolved Oxygen (Saltwater): Cape Cod to Cape Hatteras to 

rationalize lowering DO water quality standards in the LSJR in order to resubmit DEP’s 

failed, illegal, nutrient TMDL recently rescinded by EPA Region IV. In its rush to lower 

water quality standards, FDEP has chosen to ignore its own words. 

In a March, 2002 report entitled, Development of Total Maximum Daily Loads and 

Pollution Load Reduction Goals for the Lower St. Johns River Basin: Plan of Study, the 

FDEP, and the St. Johns River Water Management District (SJRWMD), discusses the 

use of the EPA VP guidance for the LSJR TMDL development. When describing the use 

of the EPA document to guide the TMDL development, the agencies noted, “...Because 

it (EPA document)has been developed for the northern adjacent Virginian Province 

estuaries, which are cooler in temperature and lower in natural levels of organic carbon, 

it will be used as guidance only in the LSJR TMDL development.” Isn’t it amazing how 

FDEP’s appraisal of the methodology has changed? 

Now, FDEP has done a 180 degree about face and notes, “....because the criteria was 

based on very conservative assumptions for northern cooler waters, application of the 

criteria directly to Florida waters would be in fact protective.” What’s the basis of this 

sunny assessment? 

After reviewing the limited data contained in the public notice, it appears the DEP has 

compared a list of fish species found in the VP and the LSJR, and it has determined that 

some species used to derive the VP criteria, “are known to occur in Florida, including the 

LSJR." Well, that’s certainly reassuring. Let’s examine the species and their economic 

importance to the river. 

In the 2003 draft TMDL document, the FDEP noted there were five fish species that 

were found in both the VP and LSJR. Those five are listed in the table below. 

SPECIES COMMON 

NAME 

Syngnathus 

fuscus pipe fish 

Paralichthus 

dentatus 

summer 

flounder 

Brevoortia spp. menhaden 

Callinectes 

sapidus blue crab 

Leiostomus 

xanthurus Spot 

130 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

The draft SSAC document now notes 15 species occur in both areas. Regardless of the 

number, the argument we raised in September, 2003 is still valid. 

When one looks at the shared species list, one thing is perfectly clear--very few of them 

have a commercial value; only summer flounder and blue crab are sought by 

recreational and/or commercial interests. Although menhaden have commercial value, 

their inclusion does not increase our confidence in this methodology. Any valid 

discussion concerning reduction in DO levels, and its potential impacts on fisheries’ 

health, should feature a bias toward protecting commercially viable species, especially in 

this portion of the river. FDEP’s lack of concern about fisheries’ health is not limited to 

pelagic species. 

FDEP has made no effort to correlate invertebrate species’ occurrence in the VP and 

LSJR. This omission is telling about FDEP’s real motives; much of the research 

concerning oxygen uptake and nutrient enrichment in coastal areas, including some of 

the research cited in the original TMDL report, notes the importance of benthic 

organisms in this relationship. 

FDEP has used the VP document and made a mockery of EPA’s own guidance. The 

EPA does not claim the VP is a “one size fits all” methodology. In fact, to the contrary, it 

warns, “Risk mangers can apply the criteria to other coastal waters if they can 

scientifically determine that their location-specific biological, physical, and water quality 

conditions are comparable to those of the Virginian Province.” There is no data in the 

public notice that would lead one to believe FDEP made such a determination. 

FDEP has failed to follow the EPA’s VP guidelines in the proposed SSAC and has 

ignored the following considerations: 

o Accuracy of monitoring data- It is not clear from the DRAFT SSAC what 

monitoring data DEP used and how well hypoxia is captured in these data. 

The VP approach precautions that existing monitoring programs are not 

always accurate enough to take advantage of the protective approach. 

o Biological effects--potential biological effects are difficult to predict. DEP 

has not provided any information about what the expected range of sensitivity 

to hypoxia should be for the LSJR. As mentioned above, DEP merely relied 

on the fact that a few fish species occurred in both systems, and therefore, 

made the determination the VP guidance is appropriate. 

o Spatial extent- there is no indication from the existing condition set forth in 

the draft if there is a hypoxic area and the extent of the hypoxic area. 

o Threatened & endangered species-Absolutely no mention of whether there 

is threatened or endangered species in the river. FDEP’s selectively omits 

this issue despite the fact that the EPA specifically addresses it in the VP fact 

sheet. 

Once again, in its rush to support it’s ill-conceived, and indefensible, nutrient TMDL for 

the LSJR, FDEP has used poor, and selectively applied, scientific reasoning to justify 

weakening DO water quality standards in the lower St. Johns River. 

131 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

2. THE APPLICATION OF SINGLE DO SSAC FOR THE “LOWER ST. JOHNS 

RIVER” IS INAPPROPRIATE AND SCIENTIFICALLY INDEFENSIBLE. 

In the March, 2002 report entitled, Development of Total Maximum Daily Loads and 

Pollution Load Reduction Goals for the Lower St. Johns River Basin: Plan of Study, the 

FDEP and the SJRWMD noted: 

“The LSJR can be divided into three zones: a predominantly fresh, tidal lake-like zone 

that extends from the city of Palatka north to the mouth of Julington Creek; an 

alternatively fresh and marine, oligohaline lake-like zone extending from Julington Creek 

northward to the Fuller Warren Bridge (I-95) in Jacksonville; and a predominantly marine 

and much narrower zone downstream from this point to the mouth.” 

Simply put, the LSJR is really three distinct “ecozones”. In effect, one cannot speak 

about the LSJR as a single biological system. FDEP and SJRWMD recognized this 

situation and noted, “The change in chemical and hydrologic conditions from freshwater 

river to ocean results in an aquatic environmental gradient in which few plants or animals 

can optimally survive and thrive.” 

 

Of course, FDEP selectively ignores these differences and contrary to their own words, 

chooses to establish a “one size fits all” DO SSAC which they apply to the three 

distinctly different systems. 

FDEP and SJRWMD, in further discussions about the zones, noted, “The existence of 

these three distinct ecozones within the LSJR has important implications for the 

determination of the nutrient enrichment response continuum.” Simply put, nutrients 

entering these systems react differently. This is particularly critical to the health of the 

LSJR because the genesis of the marine TMDL evolved from the link between low DO, 

larval recruitment, maximum acute value, and the growth effects threshold. 

Rather than recognize the complexities of the LSJR, FDEP chooses to ignore it and 

blithely publish a SACC for the LSJR as if it is a homogeneous system. What is 

particularly damning about FDEP’s approach is it is scientifically indefensible, yet they 

note the proposed SSAC will, “...fully support the propagation of and maintenance of 

healthy, well-balanced community of fish and wildlife.” FDEP’s methodology is 

unconscious able. 

3. THE LSJR SSAC FAILS TO COMPLY WITH FLORIDA STATUTE § 62-

302.800 

Florida’s variance procedures for a Site Specific Alternative Criteria (SSAC) are clearly 

laid out in the Florida Administrative Code Rule 62-302.800. The LSJR Dissolved 

Oxygen SSAC fails to meet the required procedures. 

Florida asserts that the LSJR SSAC was developed in accordance with the procedures 

set forth in subsection 62-302.800(2). However, this is contrary to what is allowed under 

the provision. Therefore, FDEP should be prohibited from developing a SSAC under 

subsection 2. 

132 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

o From all indications of the DRAFT Site Specific Alternative Dissolve 

Oxygen Criteria For the Protection of Aquatic Life in the Marine Portions 

of the Lower St. Johns River (January 9, 2006)(“Draft”), the alternative 

criteria was initiated by the State and not petitioned for by an affected 

person. Subsection (2) of 62-302.800 only sets forth procedures for 

adopting an alternative water quality criteria in the situation where an 

affected person petitioned the State, “In accordance with the procedures 

set forth below, affected persons may petition....” 62-302.800(2). This 

is to be distinguished from the procedures set forth in subsection (1), 

which apply “upon petition by an affected person or upon the initiation 

of the Department.” 62-302.800(1). Therefore, the procedures in 

subsection (2) must only be used in situations where an affected person 

petitioned for the SSAC and not upon FDEP initiation. 

o Under the present circumstances the Department is prohibited from 

relying on subsection 2 for adopting alternative criteria for dissolved 

oxygen in the LSJR because the procedures set forth in subsection 2 “do 

not apply to ... criteria that apply to: ... 7. Dissolved Oxygen.” 62-

302.500(2) (d). The criterion that FDEP is seeking to get a variance from 

is the Dissolved Oxygen criteria. Therefore, the procedures set forth in 

subsection (2) do not apply. 

Because FDEP is prohibited from relying on subsection (2) (see reasons set forth 

above), the only way FDEP can establish an alternate dissolved oxygen criteria under 

these circumstances is to meet the requirements under 62-302.800(1). 

o As a threshold issue, a SSAC under subsection (1) can only be 

established “when an affirmative demonstration is made that an 

alternative criteria is more appropriate for a specified portion of water,” i.e. 

a waterbody may not meet the particular water quality criteria specified for 

its classification due to natural background conditions or man-induced 

conditions that cannot be controlled or abated. FDEP has not asserted or 

demonstrated that the natural and man made conditions of the LSJR are 

such that it is unable to meet the applicable DO criteria. The applicable 

DO criterion for Florida Class III predominantly marine waters “[s]hall not 

average less than 5.0[mg/L (milligrams per liter)] in a 24-hour period and 

shall never be less than 4.0[mg/L].” Without any affirmative demonstration 

of an inability of the LSJR to meet these requirements, FDEP cannot 

establish an alternative criterion under subsection (1). 

o Even if FDEP could meet the affirmative threshold demonstration under 

subsection, FDEP has failed to document or provide the documentation 

requirements. FDEP is required to provide: 1) a description of the 

physical nature and the water pollution sources affecting the DO in the 

LSJR; 2) a description of the historical and existing water quality of DO, 

including at a minimum spatial, seasonal, and diurnal variations; 3) a 

description of the historical and existing biology, which may be affected 

by DO; and 4) a discussion of an impacts the alternative DO criteria will 

have on the designated use and adjoining waters. FDEP has failed to 

meet any of these requirements. At most FDEP has included a short 

133 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

description of the existing conditions and an incomplete discussion of the 

potential impact of criteria on designated uses. 

Even if FDEP was able to establish alternative DO criteria under subsection (2), DEP 

has failed to meet the required procedures. 

o At the most basic level, the petitioner, (we assume DEP), must 

demonstrate that the proposed criteria would fully maintain and protect 

human health, existing uses, and the level of water quality necessary to 

protect human health and existing and designated beneficial uses. 

o Procedurally, under subsection (2) in making the demonstration that the 

alternative criteria will fully maintain and protect, the Petitioner is required 

to: 

 Assess aquatic toxicity: there is no indication that FDEP did such 

an assessment. Additionally, FDEP cannot rely on the Virginia 

Province alone because translating that approach to another 

coastal region requires additional information and analysis. 

 Risk assessment: there is no information that has been provided 

by the Department that suggests such a risk assessment has 

been completed 

 Information indicating that one or more of the assumptions used in 

the risk assessment on which the existing criteria is based are 

inappropriate to the LSJR: once again there is nothing to suggest 

that a risk assessment has been completed 

 Economic impact statement: there is no information that has been 

provided by the Department that suggests such a statement has 

been completed 

4. THE LSJR DO SSAC FAILS TO COMPLY WITH THE REQUIREMENTS OF 

THE CWA AND EPA’S CORRESPONDING GUIDANCE DOCUMENTS 

FDEP failed to comply with federal water quality standard (WQS) variance procedures. 

EPA approves State-adopted variances if “the variance is granted for a specific period of 

time and must be rejustified upon expiration but at least every 3 years...” Water Quality 

Standards Handbook, 2nd ed. at 5-12 (1993). Therefore, variances such as a SSAC are 

required to be time limited and are not intended to allow a waterbody to forgo its 

designated use. Here, FDEP’s intention for the LSJR DO SSAC does not appear to be 

temporal; rather, FDEP’s documentation implies that it intends to implement SSAC for 

an indefinite period of time, perhaps permanently. 

Because EPA requires variance procedures to demonstrate that meeting standards 

under 40 CFR 131 is unattainable, the state should have to demonstrate that meeting 

standards under 40 CFR 131 is unattainable before SSAC can be implemented. 

According to the regulations, states may remove a designated use if the state can 

demonstrate that attaining the designated use is not feasible because of: naturally 

occurring pollutant concentrations; low flow conditions or water levels; human caused 

conditions or sources of pollution that cannot be remedied or would cause more 

134 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

environmental damage to correct; hydrologic modifications; physical conditions related to 

the natural features of the water body; or controls more stringent would result in 

substantial and widespread economic and social impact. 40 C.F.R. §131.10 (g) (1-6). 

FDEP has failed to show any of these conditions exist in order to justify the 

implementation of SSAC. 

As stated above, we believe the proposed DO SSAC is scientifically indefensible, 

unwarranted, and administratively flawed. The SSAC is nothing more then FDEP’s 

attempt to overturn EPA’s recently released nutrient TMDL for the LSJR. We believe the 

EPA’s TMDL is good first step in restoring the lower St. Johns River’s health. FDEP’s 

proposed SSAC is a step backward in that effort. 

We urge the FDEP to abandon your efforts to increase allowable pollution levels in the 

St. Johns River. As we stated over two years ago, we will continue to fight to protect the 

lower St. Johns River. 

Thank you for the opportunity to comment. 

For the River, 

Neil A. Armingeon 

St. Johns Riverkeeper 

CC: Michael Howle, Esq., St. Johns Riverkeeper 

 Linda Young, Clean Water Network of Florida 

135 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Earlier Department responses to comments on SSAC 

HISTORICAL BACKGROUND AND RESPONSE SUMMARY 

FOR ESTABLISHMENT OF SITE SPECIFIC ALTERNATIVE CRITERIA 

 FOR DISSOLVED OXYGEN IN THE LOWER ST. JOHNS RIVER 

Historical Background

Rule 62-302.800(2), Florida Administrative Code (FAC), allows for the establishment of 

Site Specific Alternative Criteria using either the Indicator Species Procedure or other 

scientifically defensible methods. These SSACs comprise Type II SSACs under Rule 

62-302.800, FAC. 

The Department and St. Johns River Water Management District (SJRWMD) began 

looking at dissolved oxygen levels in the lower St. Johns River during the recent basin 

assessment for this river reach. Initially, the SJRWMD conducted data assessment and 

modeling to determine appropriate dissolved oxygen levels that were protective of 

aquatic life. The Department formally initiated rulemaking on December 16, 2005. The 

Department conducted two public workshops in Jacksonville (January 20, 2006 and April 

7, 2006). As a result of further modeling and data analysis, as well as public comments, 

the proposed site specific alternative criteria were refined. 

The proposed rule establishes site specific alternative criteria for dissolved oxygen in the 

marine portion of the lower St. Johns River from Julington Creek to the mouth of the 

river. The alternative criteria were developed using the U.S. Environmental Protection 

Agency’s (EPA) draft guidance document, Ambient Water Quality Criteria for Dissolved 

Oxygen: Cape Cod to Cape Hatteras. The criteria are intended to support a healthy 

aquatic environment and will maintain the designated use of the river. 

The proposed criteria are expressed as a minimum concentration of 4.0 mg/L, which is 

the existing minimum default criterion for Class III marine waters, and a Total Fractional 

Exposure for each annual evaluation period of not greater than 1.0. The Total Fraction 

Exposure is defined by the equation: 

Max day 55

mg/L 5.0 - 4.8

between Days

Max day 47

mg/L 4.8 - 4.6

between Days

Max day 30

mg/L 4.6 - 4.4

between Days

Max day 21

mg/L 4.4 - 4.2

between Days

Max day 16

mg/L 4.2 - 4.0

between Days

Exposure

Fractional Total <

+

<

+

<

+

<

+

< ⎟ =

⎠

⎞ ⎜

⎝

⎛

The number of days in an interval is based on the daily average Dissolved Oxygen 

concentration. 

The Total Fractional Exposure utilizes the measured larval recruitment/survival and 

growth responses of sensitive species to limit the number of days in which the dissolved

oxygen can be in each 0.2 mg/L interval between 4.0 and 5.0 mg/L. The Departm

analysis, including the derivation of thes

ent’s 

e criteria, is attached. The EPA criteria 

guidance document is also attached. 

136 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

Public Comments and Department Response

The Department conducted two public workshops (January 20, 2006 and April 7, 2006, 

both in Jacksonville, Florida). Public workshop comments from the public included: 

1. The Department is suggesting that the lower St. Johns River is the same as 

the waters between Cape Cod and Cape Hatteras (i.e., the model is not 

representative of the lower St. Johns River). 

Response: Many of the species are common to both the Cape Cod to Cape Hatteras 

area as well as the lower St. Johns River. The model has applicability in the lower St. 

Johns River. 

2. When calculating the 30-day average, what value(s) are used for daily 

values? 

Response: The 30-day average was used in the first draft version of the SSAC. The 30-

day average is no longer used in the SSAC that was approved by the ERC. (Note: This 

comment was made after the first public workshop when the 30-day average was 

proposed for inclusion as part of the SSAC. The SSAC language no longer includes the 

30-day average.) 

3. Does the SSAC development mean that Florida cannot meet water quality 

standards in the lower St. Johns River? 

Response: The SSAC was developed specifically to characterize water quality 

standards in the lower St. Johns River. It is intended to be fully protective of sensitive 

aquatic species in their most sensitive life stages. The SSAC is part of Florida’s water 

quality standards. 

4. Is it necessary to demonstrate that water quality standards cannot be met 

in order to establish a SSAC? 

Response: No, this is not part of the demonstration. 

5. Why were species used that do not occur in the lower St. Johns River? 

Response: The most sensitive species in the EPA study were chosen. Some of these 

(e.g., American Lobster) do not occur in Florida, yet the Department believes that these 

sensitive species are representative of the most sensitive organisms in the lower St. 

Johns River. The Department does not have toxicity data for every species in the river. 

6. The SSAC is an attempt to provide a “cover” for the Department’s 

proposed TMDL. 

Response: The Department disagrees. The SSAC is independent of the TMDL and is 

intended to be fully protective of aquatic life in the river. 

137 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

7. Use of the Virginian Province model is an inappropriate surrogate for the 

lower St. Johns River. 

Response: The Department disagrees. Again, the SSAC, based on the EPA model, is 

intended to be fully protective of aquatic life. Many of the species are common to both 

the Virginian Province and the lower St. Johns River. One of the principal authors of the 

EPA Virginian Province model, Dr. Glen Thursby, specifically addressed this question in 

the document, National Saltwater Criteria for Dissolved Oxygen: Potential Addenda to 

Virginian Province Saltwater Criteria for Warmer and Colder Waters (2003). Dr. Thursby 

compared two groups of genera, one at 20 degrees C and one at 26 degrees C 

(representing northern colder waters and southern warmer waters). He concluded that 

the criterion minimum concentrations (CMCs) for the two groups are “very similar, 2.36 

mg/L for the 20C group and 2.26 mg/L for the 26C group.” Dr. Thursby also compared 

populations of three species collected from the Northeast (Rhode Island) and the 

Southeast (Georgia and Florida). He found that “The exposure-response relationships 

for each species were similar in northern and southern populations.” 

8. There are a number of water bodies in Florida that do not naturally meet the 

default state dissolved oxygen criteria. The SSAC is overly conservative 

and unduly strict. 

Response: The Department agrees that the SSAC is conservative. Most water quality 

standards are conservative. Nonetheless, the Department believes that a conservative 

SSAC is necessary to ensure protection of aquatic life in the river, particularly for 

sensitive species and sensitive life stages. 

9. Will establishment of the SSAC solve the impairment problem? 

Response: No, the river will still be impaired. Restoration of the river will occur only 

after the TMDL is implemented with its nutrient load reductions. 

10. Is the Total Fractional Exposure based on a calendar year? 

Response: Yes, it is based on a calendar year. 

11. How will the Clean Water Network’s lawsuit against EPA’s approval of 

Florida’s Type II SSAC language affect the lower St. Johns River SSAC? 

Response: It does not affect approval of the SSAC by the Florida Environmental 

Regulation Commission (Note: this comment was made at the second workshop which 

occurred a month prior to EPA’s formal approval of the Type II SSAC language. EPA 

approved the Type II language on May 11, 2006.) 

12. Was the SSAC developed specifically for the Department’s TMDL using the 

TMDL as a target? 

Response: No, the SSAC was developed independent of any TMDL. 

Shortly after the second public workshop, several editorials appeared in newspapers 

around the state, including the Florida Times Union. The Florida Times Union editorial 

138 

Florida Department of Environmental Protection 
FINAL TMDL Report: Lower St. Johns Basin, Lower St. Johns River, Nutrients 

by Ron Littlepage (attached) contained several erroneous statements that elicited 

several dozen emails sent to the Department and the Florida Environmental Regulation 

Commission (emails attached). The Department sent out a fact sheet to emailers in an 

attempt to correct the erroneous information (Frequently Asked Questions fact sheet 

attached). At the time the editorial was published, the river had begun experiencing 

algal blooms. Many of the public were under the mistaken notion that the Department 

was proposing to allow an additional one million tons of nitrogen into the river beyond 

what was already allowed. Many emailers took strong exception to this erroneous 

statement. 

Written Correspondence

Several letters were also submitted to the Department (attached). First, comments 

dated April 28, 2006 from the Clean Water Network (CWN) (also representing St. Johns 

Riverkeeper and Mid-Atlantic Environmental Law Center) are summarized: 

1. It is inappropriate to develop a SSAC for Dissolved Oxygen in the lower St. 

Johns River using the Environmental Protection Agency’s (EPA) approach 

for the Virginian Province (VP). 

Response: The Department consulted informally with one of the principal authors of the 

EPA study, Dr. Glen Thursby, in developing the SSAC for the lower St. Johns River. 

This issue was addressed in the report by Dr. Thursby, titled National Saltwater Criteria 

for Dissolved Oxygen: Potential Addenda to Virginian Province Saltwater Criteria for 

Warmer and Colder Waters (2003). There has been no evidence presented that the 

SSAC is NOT protective of aquatic life in the lower St. Johns River. The CWN states 

that they reject “FDEP’s theory that the St. Johns River is exactly like the VP...” The 

Department has never claimed that the St. Johns River is exactly like the VP. 

Nonetheless, the methodology has application in the lower St. Johns River. 

The CWN further compares fish species common to both the VP and the lower St. Johns 

River, noting that “very few of them have a commercial value”. The CWN also asserts 

that “Any valid discussion concerning reduction in DO levels, and its potential impacts on 

fisheries’ health, should feature a bias toward protecting commercially viable species, 

especially in this portion of the river.” The Department disagrees with this statement. 

The Department selected the most sensitive species in the EPA model in an attempt to 

be most protective of all species, not just the commercial species. Both commercial and 

non-commercial species are protected under the SSAC. 

The CWN states: 

FDEP has used the VP document and made a mockery of EPA’s own guidance. 

The EPA does not claim the VP is a “one size fits all” methodology. In fact, to the 

contrary, it warns, “Risk mangers (sic) can apply the criteria to other coastal 

waters if they can scientifically determine that their location-specific biological, 

physical, and water quality conditions are comparable to the Virginian Province.” 

There is no data in the recent public notice that would lead one to believe FDEP 

made such a determination. 

The Department agrees that the VP is not a “one size fits all” methodology. The 

Department, however, did conduct a comparison of the VP and the lower St. Johns 

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River. Furthermore, the Department consulted with the author of the EPA methodology 

to ensure that it was appropriate for the lower St. Johns River. 

The CWN then states: 

FDEP has failed to follow the EPA’s VP guidelines in the proposed SSAC and 

has ignored the following considerations: 

° Accuracy of monitoring data – The only monitoring data DEP used was from 

two real time monitors near Jacksonville. It is not clear from the DRAFT 

SSAC how well hypoxia is captured in these data. The VP approach 

precautions that existing monitoring programs are not always accurate 

enough to take advantage of the protective approach. 

° Biological effects – potential biological effects are difficult to predict. DEP has 

not provided any information about what the expected range of sensitivity to 

hypoxia should be for the LSJR. As mentioned above, DEP merely relied on 

the fact that a few fish species occurred in both systems, and therefore, made 

the determination the VP guidance is appropriate. 

° Spatial extent – there is no indication from the existing condition set forth in 

the draft if there is a hypoxic area and the extent of the hypoxic area. 

° Threatened and endangered species – Absolutely no mention of whether 

there is threatened or endangered species in the river. FDEP’s (sic) 

selectively omits this issue despite the fact that the EPA specifically 

addresses it in the VP fact sheet. 

The Department used all the monitoring data available. While it is true that there are 

currently only two continuous monitoring stations in the LSJR, the Department is 

pursuing the establishment of additional continuous monitoring stations. Regarding 

hypoxia, the Department has already established that the LSJR is impaired for nutrients 

and experiences algal blooms. Implementation of a TMDL is intended, in part, to 

eliminate hypoxic episodes. The SSAC is not intended to maintain depressed levels of 

dissolved oxygen. On the contrary, the SSAC is intended to protect all aquatic species 

in the marine portions of the river, including the most sensitive species. 

The Department looked at the potential occurrence of threatened and endangered 

species in the river. There are two gill-breathing species that may occur in the LSJR: 

Smalltooth Sawfish (Pristis pectinata) and Shortnose Sturgeon (Acipenser brevirostrum). 

Both species have a wide range of occurrence along the Atlantic seaboard and are both 

Federally listed as endangered. Both species have suffered historically from overharvesting and habitat loss. Sturgeon studies (Jenkins et al. 1994; Secor & Niklitschek 

2001; Campbell & Goodman 2003) have indicated that sturgeon are sensitive to low 

dissolved oxygen levels. However, these studies have shown that sturgeon mortality 

occurs at dissolved oxygen levels below 3.5 mg/L. The Campbell and Goodman (2003) 

study looked specifically at low dissolved oxygen level toxicity on juvenile Shortnose 

Sturgeon. Between 22 degrees C and 26 degrees C, they found a geometric mean 

LC50 of 2.27 mg/L, while a higher temperature (29 degrees C) resulted in an LC50 of 

3.1 mg/L. The Department’s SSAC has a minimum level set at 4.0 mg/L. 

2. The application of a single SSAC for dissolved oxygen, applicable to the 

whole of the “Lower St. Johns River”, is inappropriate and scientifically 

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indefensible. 

Response: Contrary to what the CWN states, the Department’s SSAC only applies to 

the marine portions of the LSJR. The freshwater/saltwater interface moves in response 

to tides, river flows, droughts, and other factors. The SSAC does not apply to the 

freshwater portion of the river. The Department’s SSAC replaces the statewide default 

dissolved oxygen criterion of a 4.0 mg/L minimum and a daily average of 5.0 mg/L due 

to site specific characteristics, replacing it instead with a 4.0 mg/L minimum and a Total 

Fractional Exposure between 4.0 mg/L and 5.0 mg/L. The Department finds this 

approach fully appropriate and scientifically defensible and disagrees with CWN’s 

statement. 

3. The proposed SSAC for dissolved oxygen requires real time water quality 

data that does not currently exist. 

Response: There are presently two continuous sampling stations in the LSJR. One of 

these stations is located in the portion of the river that has exhibited problems with DO in 

the past. The Department believes that these sampling stations will provide sufficient 

DO data to ensure protection of the LSJR. The Department is working on establishing 

additional continuous monitoring stations in the LSJR. 

The CWN asks a number of questions in this section of their letter: (1) How will the 

exposure estimates be computed if DO values are not available? (2) How many 

additional monitoring sites will be required? (3) Where will additional sites be located? 

(4) Who will maintain these sites? (5) Will DEP staff compute the fractional exposures on 

a daily basis? (6) What happens when the fractional exposures exceed one? (7) Will 

discharges to the LSJR be halted? 

The Department expects that there will be sufficient DO values to ensure compliance 

with the SSAC. There will be no additional requirement for monitoring sites, although 

the Department is working toward the establishment of additional sites. Additional sites 

will provide a more robust data set, but are not essential toward determining compliance. 

Any additional sites will most likely be maintained either by FDEP or the St. Johns River 

Water Management District. The Department will compute the fractional exposures on a 

daily basis (per calendar year) to ensure compliance with state water quality standards. 

If the SSAC is exceeded, the Department will take appropriate action to ensure 

compliance. This could potentially include revision of the TMDL for nutrients. 

4. The FDEP has failed to demonstrate that alternative criteria are even 

warranted for the lower St. Johns River. 

Response: The Department has noted that a continuous DO level of 5.0 mg/L is 

potentially unlikely during the hot summer months under certain conditions. The SSAC 

is warranted. It is protective of aquatic life. 

5. Although the FDEP has attempted to amend section 62-302.800 of the 

Florida Administrative Code to permit the agency to develop site specific 

alternative criteria for DO, the amendments should be considered effective 

until FDEP has obtained necessary formal approval from the EPA. 

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Response: This comment is now moot. In a letter dated May 11, 2006, EPA formally 

approved changes to Florida’s water quality standards that now allow for the 

development of a Type II SSAC for dissolved oxygen. 

6. Like the initial SSAC for the St. Johns River, the amended SSAC similarly 

fails to comply with section 62-302.800 of the Florida Administrative Code. 

Response: CWN maintains that the Department is precluded from initiating rulemaking 

itself to establish a Type II SSAC. This is an erroneous assertion. The Department can 

initiate rulemaking to amend any of its rules, following established procedures in the 

Florida Administrative Procedures Act (Chapter 120, Florida Statutes). The Department 

has followed all appropriate rulemaking steps in accordance with state law. 

7. The SSAC for dissolved oxygen in the lower St. Johns River fails to meet 

the relevant EPA standards and guidelines for variances from state water 

quality standards for (sic). 

Response: The CWN mistakenly believes that Florida’s SSACs constitute Federal 

variances. The SSAC developed for the LSJR is fully consistent with Federal Site 

Specific Criteria. These criteria are not variances as described under the EPA’s Water 

Quality Standards Handbook. 

 

The Department received written correspondence, dated April 13, 2006, from the 

Jacksonville Electric Authority (JEA). JEA’s comments are summarized: 

1. JEA believes that the SSAC is overly conservative. They believe that “the 

fundamental site-specific reason for adopting a DO SSAC for the Lower St. 

Johns River is that the state-side standard is substantially more stringent 

than needed to fully protect its designated uses.” JEA notes that the SSAC 

may be “substantially more stringent than necessary”. 

Response: The Department agrees that the SSAC is conservative, but that 

conservatism is needed in order to fully protect aquatic life in all its life stages. 

2. JEA notes an absence of “a description of the historical and existing 

biology, including variations, which may be affected by the parameter of 

concern.” JEA requests that the report be “strengthened by incorporating 

background information on status and trends in the indigenous biological 

communities, and their relationship (if any) to fluctuations in DO in the 

Lower St. Johns River”. 

Response: As JEA mentioned in their comments, 15 of the 23 species used in EPA’s 

VP DO assessment occur in the LSJR. The river is currently impaired. The current 

status and trends in the river are not indicative of a healthy riverine system. The 

Department believes that the SSAC will fully protect aquatic life and the river’s 

designated use. 

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3. JEA believes that the use of a default minimum of 4.0 mg/L is arbitrary. 

JEA asks why 4.0 mg/L was chosen for the Criterion Minimum 

Concentration (CMC) instead of a criterion developed using a scientific 

methodology, noting, in particular, that the CMC developed by EPA for the 

Virginian Province is 2.3 mg/L. 

Response: The Department believes that the default minimum of 4.0 mg/L is necessary. 

For example, studies on sturgeon have shown adverse effects at DO levels of 3.5 mg/L 

and below. The SSAC is intended to be fully protective of all sensitive aquatic life and 

life stages. 

4. JEA objects to the use of a species (American Lobster, Homarus 

americanus) not found in Florida. They propose that a species of mud crab 

be substituted instead. 

Response: The Department deliberately chose the most sensitive species in the EPA 

study. The Department believes that there are species with similar needs and 

requirements in the LSJR and that the American Lobster is an appropriate substitute in 

the absence of more data. 

5. JEA strongly recommends “that the Department take into account how the 

proposed rule would affect the Total Maximum Daily Load (TMDL) of 

nutrients that the river could accommodate, and provide a clear discussion 

of the economic impacts that the rule might have, to the extent that the 

TMDL needed to comply with it would be more stringent than the TMDL the 

Department adopted for the river in 2003.” 

Response: The SSAC was developed independent of any TMDL. The SSAC was 

developed to be fully protective of the most sensitive aquatic life and the most sensitive 

aquatic life stages. It is inappropriate to use a TMDL to develop a SSAC. 

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References 

Campbell, J.G., and L.R. Goodman. 2003. Acute sensitivity of juvenile shortnose 

sturgeon to low dissolved oxygen concentrations. Draft report for Gulf Ecology 

Division, National Health and Environmental Effects Research Laboratory, U.S. 

Environmental Protection Agency. 

Jenkins, W.E., T.I.J. Smith, L.D. Heyward, and D.M. Knott. 1994. Tolerance of 

shortnose sturgeon, Acipenser brevirostrum, juveniles to different salinity and 

dissolved oxygen concentrations. Proc. Annu. Conf. Southeast. Assoc. Game Fish 

Comm.

Secor, D.H., and E.J. Niklitschek. March 29, 2001. Hypoxia and sturgeons. Report to 

the Chesapeake Bay Program Dissolved Oxygen Criteria Team. 

Thursby, G.B. October 7, 2003. National saltwater criteria for dissolved oxygen: 

Potential addenda to Virginian Province saltwater criteria for warmer and colder 

waters. AED-03-113, USEPA. 

U.S. Environmental Protection Agency. 2000. Ambient aquatic life water quality criteria 

for dissolved oxygen (saltwater): Cape Cod to Cape Hatteras. PA-822-R-00-012. 

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Florida Department of Environmental Protection 

Attachments 

1. Revisions to Rule 62-302.800, F.A.C. 

2. Site Specific Alternative Dissolved Oxygen Criterion to Protect Aquatic Life in the 

Marine Portions of the Lower St. Johns River Technical Support Document

(Department and SJRWMD, April 28, 2006). 

3. Ambient Aquatic Life Water Quality Criteria for Dissolved Oxygen (Saltwater): 

Cape Cod to Cape Hatteras (U.S. Environmental Protection Agency, Office of 

Water, PA-822-R-00-012, 2000). 

4. National Saltwater Criteria for Dissolved Oxygen: Potential Addenda to Virginian 

Province Saltwater Criteria for Warmer and Colder Waters (U.S. Environmental 

Protection Agency, National Health and Environmental Effects Research 

Laboratory, AED-03-113, 2003). 

5. Editorial by Ron Littlepage, Florida Times Union, May 12, 2006. 

6. Emails sent to the Department and Environmental Regulation Commission. 

7. Summary of major issues raised in emails from the public (Department, May 17, 

2006). 

8. Lower St. Johns River TMDL/SSAC Frequently Asked Questions (Department, 

May 2006). 

9. Florida Times Union Editorial Board Questions and Department Response 

(Department and SJRWMD, June 16, 2006). 

10. Written correspondence sent to the Department. 
Florida Department of Environmental Protection 

Division of Water Resource Management 

Bureau of Watershed Management 

2600 Blair Stone Road, Mail Station 3565 

Tallahassee, Florida 32399-2400 

www.dep.state.fl.us/water/