FINAL 

FLORIDA DEPARTMENT OF ENVIRONMENTAL PROTECTION 

Division of Water Resource Management, Bureau of Watershed Management

NORTHEAST DISTRICT • OCKLAWAHA BASIN 

TMDL Report 

Nutrient TMDL for Alachua Sink, 

WBID 2720A 

Xueqing Gao, Douglas Gilbert, 

and Wayne Magley 

April 4, 2006 
i TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Acknowledgments 

This study could not have been accomplished without significant contributions from staff 

in the Florida Department of Environmental Protection’s (Department) Watershed 

Assessment Section. The authors particularly appreciate Barbara Donner’s 

contributions. Most of the basin delineations and land use aggregations, and much of 

the data gathering, are a result of her efforts. The Department also recognizes the 

substantial support and assistance provided by the St. Johns River Water Management 

District staff, staff of the Gainesville Regional Utilities, Alachua County Environmental 

Protection Department staff, city of Gainesville stormwater staff, and Jim Weimer, 

Biologist at the Department’s Paynes Prairie Park. Their contributions towards 

understanding the issues, history, and processes at work in the Alachua Sink watershed 

were invaluable. 

Editorial assistance provided by 

Daryll Joyner, Jan Mandrup-Poulsen, and Linda Lord 

For additional information on the watershed management approach and impaired 

waters in the Ocklawaha Basin, contact 

Wayne Magley 

Florida Department of Environmental Protection 

Bureau of Watershed Management 

Watershed Planning and Coordination Section 

2600 Blair Stone Road, Mail Station 3555 

Tallahassee, FL 32399-2400 

Email: wayne.magley@dep.state.fl,us

 Phone: (850) 245-8463, SunCom: 205-8463 

Fax: (850) 245-8356 

Access to all data used in the development of this report can be obtained by 

contacting 

Wayne Magley 

Florida Department of Environmental Protection 

Bureau of Watershed Management 

Watershed Planning and Coordination Section 

2600 Blair Stone Road, Mail Station 3555 

Tallahassee, FL 32399-2400 

Email: wayne.magley@dep.state.fl.us 

Phone: (850) 245-8463, SunCom: 205-8463 

Fax: (850) 245-8356 

 i
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients ii

Contents 

CHAPTER 1: INTRODUCTION ........................................................................... 1

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

1.2 Identification of Waterbody ................................................................................. 1

CHAPTER 2: STATEMENT OF PROBLEM ........................................................ 4

2.1 Current Trophic Status of Alachua Sink .............................................................. 4

CHAPTER 3: DESCRIPTION OF APPLICABLE WATER QUALITY 

STANDARDS AND CRITERIA ................................................... 10

CHAPTER 4: ASSESSMENT OF SOURCES ................................................... 12

4.1 Overview of the TMDL Development Process.................................................. 12

4.2 Types of Sources ................................................................................................ 12

4.3 Estimating TN and TP Loadings Using the WMM ............................................. 13

4.3.1 Breakdown of Sub-basins and Land Uses ..................................................... 13

4.3.2 Potential Sources of TN and TP in the Alachua Sink Watershed ................... 15

4.4 Estimating Watershed Loadings Using the WMM ........................................... 15

4.4.1 Estimating Sub-basin Loadings Using the WMM ........................................... 16

4.4.2 Data Required for Estimating TN and TP Loadings from Point and 

Nonpoint Sources Using the WMM............................................................... 18

4.4.3 WMM Flow Calibration ................................................................................... 24

4.4.4 WMM Flow Simulation .................................................................................... 24

4.4.5 WMM TN and TP Loading Estimation ............................................................ 25

CHAPTER 5: DETERMINATION OF ASSIMILATIVE CAPACITY ................... 37

5.1 Lake Modeling Using the Bathtub Model.......................................................... 37

5.1.1 Bathtub Eutrophication Model ........................................................................ 37

5.1.2 Data Requirements for Running Bathtub........................................................ 38

5.1.3 Calculation of the Trophic State Index............................................................ 39

5.2 TMDL Scenario Development for Alachua Sink ............................................... 39

5.3 Establishing the Relationship between TN and TP Loading to Alachua 

Sink and In-lake Concentrations ....................................................................... 40

5.3.1 Atmospheric Loading of TN and TP into Alachua Sink and Alachua 

Lake .............................................................................................................. 40

5.3.2 Simulated TN, TP, and Chla Concentrations in Alachua Lake Using the 

Bathtub Model............................................................................................... 40

5.3.3 Data Required for the Simulation of TN and TP Concentrations in 

Alachua Lake ................................................................................................ 40

 ii
iii TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

5.3.4 Calibrating Bathtub Using the TN and TP Concentrations of Alachua 

Lake Measured in 2003 ................................................................................ 42

5.3.5 Simulation of TN and TP concentrations of Alachua Lake for 2004 ............... 45

5.3.6 Simulation of TN and TP concentrations of Alachua Lake from 2000 

through 2002................................................................................................. 47

5.4 Bathtub Calibration for the Alachua Sink Model ............................................. 47

5.3.1 Data Required for Calibrating the Bathtub Model for Alachua Sink................ 47

5.3.2 Determination of Wet and Dry Periods for Model Simulation and TMDL 

Development................................................................................................. 57

5.3.3 Evaluating the Background TSI of Alachua Sink ............................................ 61

5.3.4 Summary of TN and TP Loading for Current and Background 

Conditions ..................................................................................................... 64

CHAPTER 6: DETERMINATION OF THE TMDL.............................................. 68

6.1 Expression and Allocation of the TMDL ........................................................... 68

6.2 Load Allocation ................................................................................................... 69

6.3 Wasteload Allocation ......................................................................................... 69

6.3.1 NPDES Wastewater Discharges .................................................................... 69

6.3.2 NPDES Stormwater Discharges ..................................................................... 70

6.4 Margin of Safety ................................................................................................... 70

CHAPTER 7: NEXT STEPS: IMPLEMENTATION PLAN DEVELOPMENT 

AND BEYOND ............................................................................ 71

7.1 Basin Management Action Plan ........................................................................ 71

REFERENCES ................................................................................................... 72

APPENDICES 75

Appendix A: Background Information on Federal and State Stormwater 

Programs ............................................................................................................. 75

Appendix B: Paynes Prairie Elevation, Area, and Volume Information ............... 76

Appendix C: Responses to Comments................................................................... 79

 iii
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients iv

List of Tables 

Table 1. Annual averages of TN, TP, chla, and TSI values of Alachua Sink, 

2000–02 ....................................................................................................... 5

Table 2a. Seasonal variation of TN, TP, chla, and TSI of Alachua Sink .................... 5

Table 2b. TN concentration of Alachua Sink in 2003 (all values in mg/L) ................ 6

Table 2c. TP concentration of Alachua Sink in 2003 (all values in mg/L) ................. 6

Table 2d. Chla concentration of Alachua Sink in 2003 (all values in 

micrograms per liter [μg/L]) ...................................................................... 6

Table 2e. Mean TN/TP ratio and TSI based on all the sampling sites in 

Alachua Sink in 2003 ................................................................................. 7

Table 2f. TN concentration of Alachua Sink in 2004 (all values in mg/L) ................. 7

Table 2g. TP concentration of Alachua Sink in 2004 (all values in mg/L) ................. 7

Table 2h. Chla concentration of Alachua Sink in 2004 (all values in μg/L)............... 7

Table 2i. Mean TN/TP ratio and TSI based on all the sampling sites in 

Alachua Sink in 2004 ................................................................................. 8

Table 3. Classification of land use categories for Alachua Sink (in acres) ............ 14

Table 4. Annual precipitation at Gainesville Regional Airport, 1998–2004 ............. 19

Table 5. Annual stream flow of Sweetwater Branch at USGS Gauging 

Station 02240988, 1998–2004 .................................................................. 19

Table 6. Area of each land use category of the watershed that discharges 

into Alachua Sink through Sweetwater Branch .................................... 20

Table 7. Percent area of each land use category in each sub-basin....................... 20

Table 8. Percent directly connected impervious area for different land use 

categories ................................................................................................. 21

Table 9. EMCs of TN and TP for different land use categories ................................ 22

Table 10. Percent TP and TN in suspended form for different land use 

categories ................................................................................................. 22

Table 11. Annual average daily discharge and TN and TP concentrations in 

the discharge from the Main Street WWTP, 1998–2004 ....................... 23

Table 12. Estimated annual average daily discharge and effluent TN and TP 

concentrations for the John R. Kelly Generating Station, 1998–

2004 ........................................................................................................... 24

Table 13. Results of the WMM dry period water quantity calibration for the 

USWB, 1998–2004 .................................................................................... 24

Table 14. Estimated annual flow (ac-ft/yr) for each sub-basin, 2000–04 ................ 24

Table 15. Predicted TN and TP loadings (pounds per year [lbs/yr]) for each 

sub-basin, 2000–04 .................................................................................. 25

Table 16a. Contribution of TN (lbs/yr) from different sources in the 

watershed that discharged into Alachua Sink through 

Sweetwater Branch in 2000..................................................................... 25

Table 16b. Contribution of TN (lbs/yr) from different sources in the 

watershed that discharged into Alachua Sink through 

Sweetwater Branch in 2001..................................................................... 26

 iv
v TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 16c. Contribution of TN (lbs/yr) from different sources in the 

watershed that discharged into Alachua Sink through 

Sweetwater Branch in 2002..................................................................... 26

Table 16d. Contribution of TN (lbs/yr) from different sources in the 

watershed that discharged into Alachua Sink through 

Sweetwater Branch in 2003..................................................................... 27

Table 16e. Contribution of TN (lbs/yr) from different sources in the 

watershed that discharged into Alachua Sink through 

Sweetwater Branch in 2004..................................................................... 27

Table 17a. Contribution of TP (lbs/yr) from different sources in the 

watershed that discharged into Alachua Sink through 

Sweetwater Branch in 2000..................................................................... 28

Table 17b. Contribution of TP (lbs/yr) from different sources in the 

watershed that discharged into Alachua Sink through 

Sweetwater Branch in 2001..................................................................... 28

Table 17c. Contribution of TP (lbs/yr) from different sources in the 

watershed that discharged into Alachua Sink through 

Sweetwater Branch in 2002..................................................................... 29

Table 17d. Contribution of TP (lbs/yr) from different sources in the 

watershed that discharged into Alachua Sink through 

Sweetwater Branch in 2003..................................................................... 29

Table 17e. Contribution of TP (lbs/yr) from different sources in the 

watershed that discharged into Alachua Sink through 

Sweetwater Branch in 2004..................................................................... 30

Table 18a. Contribution of TN (lbs/yr) from different sources in the 

watershed that discharged into Alachua Lake in 2000 ........................ 30

Table 18b. Contribution of TN (lbs/yr) from different sources in the 

watershed that discharged into Alachua Lake in 2001 ........................ 31

Table 18c. Contribution of TN (lbs/yr) from different sources in the 

watershed that discharged into Alachua Lake in 2002 ........................ 31

Table 18d. Contribution of TN (lbs/yr) from different sources in the 

watershed that discharged into Alachua Lake in 2003 ........................ 32

Table 18e. Contribution of TN (lbs/yr) from different sources in the 

watershed that discharged into Alachua Lake in 2004 ........................ 32

Table 19a. Contribution of TP (lbs/yr) from different sources in the 

watershed that discharged into Alachua Lake in 2000 ........................ 33

Table 19b. Contribution of TP (lbs/yr) from different sources in the 

watershed that discharged into Alachua Lake in 2001 ........................ 33

Table 19c. Contribution of TP (lbs/yr) from different sources in the 

watershed that discharged into Alachua Lake in 2002 ........................ 34

Table 19d. Contribution of TP (lbs/yr) from different sources in the 

watershed that discharged into Alachua Lake in 2003 ........................ 34

Table 19e. Contribution of TP (lbs/yr) from different sources in the 

watershed that discharged into Alachua Lake in 2004 ........................ 35

Table 20. Atmospheric loading of TN and TP (lbs/yr) into Alachua Lake and 

Alachua Sink, 2000–04 ............................................................................ 40

Table 21. Physical characteristics of Alachua Lake, 2000–04 ................................. 41

Table 22. Precipitation and evaporation (m/yr), 2000–04 ......................................... 42

 v
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients vi

Table 23. Alachua Lake flow and the TN and TP concentrations of different 

sources in 2003 ........................................................................................ 42

Table 24. TN and TP concentrations of Alachua Lake in 2003 (all values in 

mg/L) ......................................................................................................... 43

Table 25. Bathtub calibration for Alachua Lake in 2003).......................................... 45

Table 26. Alachua Lake flow and TN and TP concentrations of different 

sources in 2004 ........................................................................................ 46

Table 27. TN and TP concentrations of Alachua Lake in 2004 (all values in 

mg/L) ......................................................................................................... 46

Table 28. Bathtub calibration for Alachua Lake in 2004 ........................................... 46

Table 29. Alachua Lake flow, and TN and TP concentrations of different 

sources, 2000–02 ..................................................................................... 47

Table 30. Bathtub-simulated TN and TP concentrations of Alachua Lake, 

2000–02 ..................................................................................................... 47

Table 31. Physical characteristics of Alachua Sink, 2000-–04................................. 48

Table 32. Physical characteristics of Alachua Sink in 2003 and 2004 .................... 50

Table 33. Bathymetry data for Alachua Sink ............................................................. 50

Table 34. Calculating the volume, surface area, and mean depth of Alachua 

Sink, 2000–02 ........................................................................................... 51

Table 35. Precipitation and evaporation (m/yr) ......................................................... 51

Table 36. Measured TN, TP, and Chla concentrations of Alachua Sink .................. 51

Table 37. Alachua Sink flow and TN and TP concentrations of different 

sources, 2000–02 ..................................................................................... 52

Table 38. Alachua Sink flow and TN and TP concentrations of different 

sources in 2003 ........................................................................................ 52

Table 39. Alachua Sink flow and TN and TP concentrations of different 

sources in 2004 ........................................................................................ 52

Table 40. Bathtub calibration results for Alachua Sink ............................................ 53

Table 41. Annual average flow and chla concentrations in Sweetwater 

Branch and Alachua Lake used to calculate Ain ................................... 56

Table 42. Percentile flow at the Sweetwater Branch gauge with and without 

the Main Street WWTF, 1998–2004 ......................................................... 61

Table 43. Background flow and TN and TP concentrations of surface runoff 

into Alachua Sink and Alachua Lake in a dry year ............................... 62

Table 44. Background flow and TN and TP concentrations of surface runoff 

into Alachua Sink and Alachua Lake in a wet year ............................... 62

Table 45. Simulated natural background TN and TP concentrations for 

Alachua Lake in dry and wet years ........................................................ 63

Table 46. Simulated background TN, TP, and chla concentrations and TSI 

for Alachua Sink in dry and wet years ................................................... 64

Table 47. Alachua Sink TN and TP loadings (lbs/yr) from point and 

nonpoint sources under current and background conditions ............ 65

Table 48. TN and TP loadings from different sources resulting in the target 

TSI (lbs/yr) ................................................................................................ 67

Table 49. TMDL Components ...................................................................................... 69

 vi
vii TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

List of Figures 

Figure 1. General location and land uses for the Alachua Sink watershed ............. 3

Figure 2. Locations of JEA sampling sites .................................................................. 9

Figure 3. Delineation of the Paynes Prairie watershed ............................................ 13

Figure 4. Location of the USGS gauging station (Site ID: 02240988) used 

for flow calibration ................................................................................... 18

Figure 5. Bathtub conceptual scheme ....................................................................... 37

Figure 6. TN and TP Load in Alachua Lake in 2003 .................................................. 43

Figure 7. Correlation between the surface elevation of Alachua Sink and 

total flow into the waterbody .................................................................. 49

Figure 8. Correlation between water residence time τo and total flow into 

Alachua Sink ............................................................................................ 54

Figure 9. Annual rainfall at Gainesville, 1897–2004 .................................................. 58

Figure 10. Running three-year average rainfall for Gainesville ............................... 59

Figure 11a. Daily flow (cfs) on Sweetwater Branch near Williston Road, 

1998–2004 ................................................................................................. 60

Figure 11b. Cumulative frequency flow plot for Sweetwater Branch with 

and without the Main Street WWTP ........................................................ 60

Figure 12. Correlation plot of TSINUT versus reduction from the current drycondition case .......................................................................................... 66

Figure 13. Correlation plot of TSINUT versus reduction from the current wetcondition case .......................................................................................... 66

Web sites 

Florida Department of Environmental Protection, Bureau of 

Watershed Management 

Total Maximum Daily Load (TMDL) Program 

http://www.dep.state.fl.us/water/tmdl/index.htm

Identification of Impaired Surface Waters Rule 

http://www.dep.state.fl.us/water/tmdl/docs/AmendedIWR.pdf

STORET Program 

http://www.dep.state.fl.us/water/storet/index.htm

2004 305(b) Report 

http://www.dep.state.fl.us/water/docs/2004_Integrated_Report.pdf

Water Quality Status Reports and Assessment Reports 

http://www.dep.state.fl.us/water/tmdl/stat_rep.htm

Allocation Technical Advisory Committee (ATAC) Report 

http://www.dep.state.fl.us/water/tmdl/docs/Allocation.pdf

 vii
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

 

viii

viii

U. S. Environmental Protection Agency 

Region 4: Total Maximum Daily Loads in Florida 

http://www.epa.gov/region4/water/tmdl/florida/

National STORET Program 

http://www.epa.gov/storet/
1 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Chapter 1: INTRODUCTION 

1.1 Purpose of Report 

This report documents the development of the nutrient total maximum daily load (TMDL) for 

Alachua Sink. Located in central Florida near Gainesville (Figure 1), Alachua Sink was verified 

as impaired by nutrients using the methodology in the Identification of Impaired Surface Waters 

Rule (IWR), Rule 62-303, Florida Administrative Code [F.A.C.]), and was included on the 

Verified List of impaired waters for the Ocklawaha Basin that was adopted by Secretarial Order 

on August 28, 2002. 

Once a waterbody or waterbody segment has been verified as impaired and referenced in the 

Secretarial Order adopting the Verified List, work on establishing the TMDL begins. The TMDL 

process establishes the allowable loadings of pollutants or other quantifiable parameters for a 

waterbody based on the relationship between pollution sources and instream water quality 

conditions, so that states can establish water quality–based controls to reduce pollution from 

both point and nonpoint sources and restore and maintain the quality of their water resources 

(U. S. Environmental Protection Agency [EPA], 1999). 

1.2 Identification of Waterbody 

Alachua Sink (WBID 2720A) is located on the northern edge of Paynes Prairie, south of the city 

of Gainesville, and approximately 2.5 miles east of U. S. 441. It consists of a small lake, with a 

corresponding solution sink that recharges the Floridan aquifer (Jones, Edmunds & Associates, 

Inc. [JEA], 2003). Alachua Sink has a surface area of about 13.5 acres and a mean depth of 

around 1 meter (Figures 1 and 2). 

Alachua Sink lies in a physiographic region of the state known as the Central Valley (McGrail et 

al., 1998). The center of Alachua Sink is located at latitude 290 36’ 18” N. and longitude 820 18’ 

9” W. (Figure 1). The dominant, underlying geologic component of the area is the Ocala 

limestone formation, with younger, overlying terrace deposits of undifferentiated sediments, 

sand, and clayey sand (Gottgens and Montague, 1988). The Ocala formation is a soft, porous 

limestone, interbedded with dense, hard limestone and dolomite (Clark et al., 1964). Sink 

formations have occurred in the area through subterranean erosion by ground water solution of 

the limestone. 

The surrounding drainage basin for Alachua Sink is approximately 2,758 acres. There are two 

well-defined inflows into Alachua Sink: Sweetwater Branch and a culverted canal that connects 

Alachua Lake to Alachua Sink (a combined drainage area of 39,373 acres). Alachua Lake is 

the inundated portion of Paynes Prairie. Presumably, any runoff coming into Paynes Prairie that 

does not sink into the ground is incorporated into Alachua Lake and some portion is shunted to 

Alachua Sink during high-water conditions. Major sources of flow to Paynes Prairie include 

Bivens Arm, Prairie Creek (which connects the prairie to Newnans Lake), and Camps Canal. 

Based on long-term U. S. Geological Survey (USGS) flow measurements (1942–91), about 41% 

of the flow from Newnans Lake goes south into Paynes Prairie, and the rest flows towards 

Orange Lake by way of Camps Canal (Gottgens and Montague, 1988). As shown in Figure 2,

the Alachua Sink waterbody has an outlet stream that flows to the primary sink feature. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 2

Historically, Alachua Sink was used for recreation (ACLD, 2003). More recently, Alachua Sink 

has become dominated by a thriving alligator population that prohibits its use for this purpose. 

The increased urbanization of the nearby city of Gainesville has contributed pollutants through 

atmospheric deposition, stormwater runoff, and point source discharges. One domestic 

wastewater facility and one industrial wastewater facility are permitted to discharge effluent to 

Sweetwater Creek, which is connected to Alachua Sink via a canal. Septic tanks used in less 

developed parts of Alachua Sink’s drainage may also be contributing pollutants to Alachua Sink 

via tributaries to Paynes Prairie. 

For assessment purposes, the Ocklawaha Basin has been divided into assessment polygons, 

termed waterbody segments, that are assigned unique waterbody identification numbers 

(WBIDs).1

 

 

1

 Additional information on the derivation and use of WBID numbers is provided in Documentation for the 2002 Update to the State 

of Florida’s 303(d) List, October 1, 2002; geographic information system (GIS) shapefiles of the waterbody segments are available 

at www.dep.state.fl.us/water/basin411/download.htm. 
3 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Figure 1. General location and land uses for the Alachua Sink watershed 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 4

Chapter 2: STATEMENT OF PROBLEM 

Based on the water quality data provided by the St. Johns River Water Management District 

(SJRWMD), Alachua Sink was determined to have elevated nutrient and chlorophyll a (chla) 

values, with an average Trophic State Index (TSI) score of 78 from 2000 through 2002. For this 

period, the average annual total nitrogen (TN), total phosphorus (TP), and chla concentrations 

were 4.33 milligrams per liter (mg/L), 1.279 mg/L, and 40.8 μg/L, respectively. The individual 

annual averages are provided in Table 1 and the seasonal averages in Table 2. For all years of 

record, the annual TSI was above 60. The mean color of Alachua Sink during this period was 

calculated as 106 platinum cobalt units (PCUs). 

2.1 Current Trophic Status of Alachua Sink 

The SJRWMD provided monthly TN, TP, and chla concentrations for Alachua Sink from 2000 

through 2002 (Site ID: ALACHCHAN). Quarterly mean values for TN, TP, and chla

concentrations were calculated from the monthly data, and quarterly TSIs were calculated 

based on the quarterly mean values of TN, TP, and chla concentrations. Annual mean values 

for TN, TP, chla, and TSI represented the mean of quarterly averages of these parameters. 

It is important to note that the procedures for calculating the annual or seasonal average TSIs 

for assessment purposes (Tables 1 and 2) are necessarily different from those used to 

calculate the annual or seasonal averages from modeling results (Table 38). The major 

difference is that the assessment protocol calls for determining a TSI for each quarter based on 

that quarter’s TN, TP, and chla concentrations, and then averaging the four quarterly TSIs to 

produce the annual average. In contrast, a model run on an annual basis will produce a single 

set of annual average concentrations from which the annual average TSI is calculated. The 

arable. For this reason, when comparing the annual or seasonal model TSIs with the measured 

TSIs calculated by the two different approaches are not necessarily comp data, the measured 

data were averaged for the entire year to produce a single set of TN, TP, and chla

concentrations used to produce the measured annual average TSI. For Alachua Sink, the 

annual average TSI following the assessment protocol is 78, while the annual average TSI used 

for comparison with the model results is 81. 

The seasonal trend of TN, TP, chla, and TSI were examined by calculating the long-term 

quarterly mean values based on the quarterly mean values of each year (2000–02). Table 1

lists the individual annual mean TN, TP, chla , and TSI values, and Table 2 lists the long-term 

quarterly TN, TP, chla, and TSI results. 
5 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 1. Annual averages of TN, TP, chla, and TSI values of Alachua Sink, 2000–02 

Data represent the mean ± 1SE (n=4). 

Year TN 

(mg/L) 

TP 

(mg/L) 

Chla

(μg/L) TSI 

2000 4.51± 1.04 1.182 ± 0.243 46.3 ± 21.3 79 ± 2 

2001 4.82 ± 0.81 1.353 ± 0.109 33.2 ± 15.3 77 ± 3 

2002 3.65 ± 0.39 1.302 ± 0.229 43.0 ± 15.1 77 ± 3 

Mean 4.33 ± 0.35 1.279 ± 0.051 40.8 ± 3.9 78 ± 1 

As shown in Table 1, no significant interyear differences were observed for TN, TP, chla, and 

TSI from 2000 through 2002. The long-term average TN/TP ratio for Alachua Sink is about 4, 

suggesting that the phytoplankton communities in the lake are nitrogen limited. This suggests 

that phytoplankton would be sensitive to further nitrogen reductions and the TMDL should 

consider nitrogen as the primary pollutant of concern. Because the long-term annual average 

color of Alachua Sink is about 106 PCUs, the IWR threshold for nutrient impairment is an annual 

average TSI of 60. Alachua Sink was verified as impaired based on annual average TSIs 

greater than 60. 

No statistically significant seasonal variation of TN, TP, chla, and TSI was observed from 2000 

through 2002 (Table 2a).

Table 2a. Seasonal variation of TN, TP, chla, and TSI of Alachua Sink 

Quarter TN 

(mg/L) 

TP

(mg/L) 

Chla

(μg/L) TSI 

1st quarter 5.06 ± 1.08 1.345 ± 0.335 26.6 ± 11.2 77 ± 2 

2nd quarter 3.26 ± 0.38 0.915 ± 0.071 66.1 ± 12.4 81 ± 2 

3rd quarter 3.75 ± 0.41 1.467 ± 0.055 50.4 ± 29.5 77 ± 5 

4th quarter 5.25 ± 1.16 1.389 ± 0.210 20.3 ± 8.4 76 ± 2 

Note: Data represent mean ±1SE; n equals 3 years (2000–02). 

No measured flow data were available at the control structure located in the channel from 

Alachua Lake to Alachua Sink from 2000 through 2002. Even though the rainfall in 2002 was 

not considered “low,” very little water was discharged into Alachua Sink from Alachua Lake 

through the control structure during this period, according to observations from local citizens. 

Therefore, the water quality data for Alachua Sink during 2000 and 2002 were considered 

representative of dry-period conditions. 

To understand the water quality condition of Alachua Sink during wet periods, further sample 

collections and water quality measurements were conducted by JEA, Inc. in 2003 (and 

subsequently in 2004). During 2003, flows from Alachua Lake into Alachua Sink increased 

dramatically over the previous three years. Water quality samples were collected from six sites 

in Alachua Sink in 2003. Figure 2 shows the locations of the sampling sites. Tables 2b, 2c, 

and 2d list tesults from the analyses completed to date. Table 2e lists the TN/TP ratios and 

TSIs calculated based on the mean TN, TP, and chla concentrations. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 6

JEA conducted three additional surveys in 2004 (February 11, 2004; May 19, 2004; and 

September 23, 2004). The Alachua County Environmental Protection Department (ACEPD) 

also conducted sampling during 2004, and these measurements were incorporated into Tables 

2f through 2i. 

Table 2b. TN concentration of Alachua Sink in 2003 (all values in mg/L) 

Sampling Date S1 S2 S3 S4 S5 S6 Mean

02/12/2003 4.640 6.930 4.820 4.680 4.680 4.880 5.105 

03/12/2003 2.904 2.949 2.926 2.922 2.899 3.123 2.954 

03/27/2003 2.572 2.510 2.604 2.695 2.585 2.492 2.576 

05/07/2003 2.090 2.155 - - - 2.293 2.179 

05/22/2003 1.780 1.770 - - - 1.780 1.777 

06/09/2003 1.825 1.681 - - - 1.813 1.773 

10/16/2003 1.200 - - - - 1.090 1.145 

12/09/2003 1.411 - - - - 1.45 1.4301 

Annual mean 2.047 2.999 3.450 3.432 3.388 2.365 2.367

Table 2c. TP concentration of Alachua Sink in 2003 (all values in mg/L) 

Sampling Date S1 S2 S3 S4 S5 S6 Mean

02/12/2003 0.96 0.96 0.93 0.96 0.96 0.96 0.96 

03/12/2003 1.13 1.14 1.12 1.16 1.14 1.13 1.14 

03/27/2003 0.65 0.70 0.65 0.67 0.66 0.66 0.67 

05/07/2003 0.44 0.47 - - - 0.52 0.48 

05/22/2003 0.21 0.22 - - - 0.22 0.22 

06/09/2003 0.21 0.23 - - - 0.22 0.22 

10/16/2003 0.08 ---- ---- ---- ---- 0.06 0.07 

12/09/2003 0.08 ---- ---- ---- ---- 0.06 0.07 

Annual mean 0.42 0.62 0.90 0.93 0.920 0.48 0.48

Table 2d. Chla concentration of Alachua Sink in 2003 (all values in micrograms per liter 

[μg/L]) 

Sampling Date S1 S2 S3 S4 S5 S6 Mean

02/12/2003 7.33 13.10 13.90 10.70 9.25 12.80 11.18 

03/12/2003 1.71 1.18 1.31 2.52 1.07 2.52 1.72 

03/27/2003 3.16 2.59 3.76 1.69 2.99 3.60 2.97 

05/07/2003 10.7 14.5 ---- ---- ---- 45.60 23.60 

05/22/2003 8.72 14.3 ---- ---- ---- 8.38 10.47 

06/09/2003 10.9 10.6 ---- ---- ---- 17.60 13.03 

10/16/2003 6.49 ---- ---- ---- ---- 1.83 4.16 

10/09/2003 3.86 ---- ---- ---- ---- 4.07 3.96 

Annual mean 5.87 9.38 6.32 4.97 4.44 12.05 8.89
7 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 2e. Mean TN/TP ratio and TSI based on all the sampling sites in Alachua Sink in 

2003 

Sampling Date TN/TP TSI

02/12/2003 5 73 

03/12/2003 3 54 

03/27/2003 4 56 

05/07/2003 5 69 

05/22/2003 8 61 

06/09/2003 8 63 

10/16/2003 16 49 

12/09/2003 17 50 

Annual mean 9 64*

*

 The values are calculated based on the annual 

average TN, TP, and chla concentrations. The 

value is not a simple mean of the TSI values for 

each sampling event. 

Table 2f. TN concentration of Alachua Sink in 2004 (all values in mg/L) 

Sampling Date S1 S2 Middle S6 Mean 

02/11/2004 1.84 2.38 2.38 2.20 

05/19/2004 1.51 1.33 2.06 1.63 

06/17/2004 1.4 1.4 

07/21/2004 1.4 1.4 

08/11/2004 1.8 1.8 

09/23/2004 2.72 2.52 2.8 2.79 2.68 

Annual mean 2.02 2.08 1.85 2.41 1.85 

Table 2g. TP concentration of Alachua Sink in 2004 (all values in mg/L) 

Sampling Date S1 S2 Middle S6 Mean 

02/11/2004 0.19 0.35 0.26 0.27 

05/19/2004 0.36 0.45 0.50 0.44 

06/17/2004 0.67 0.67 

07/21/2004 0.80 0.80 

08/11/2004 0.69 0.69 

09/23/2004 0.77 0.77 0.87 0.83 0.81 

Annual mean 0.44 0.52 0.76 0.53 0.61 

Table 2h. Chla concentration of Alachua Sink in 2004 (all values in μg/L) 

Sampling Date S1 S2 Middle S6 Mean 

02/11/2004 5.33 1.65 3.22 3.40 

05/19/2004 13.30 3.88 27.90 15.02 

06/17/2004 45.2 45.2 

07/21/2004 80.1 80.1 

08/11/2004 4.7 4.7 

09/23/2004 48.7 38.0 54.9 60.2 50.4 

Annual mean 22.4 14.5 46.2 30.4 33.1 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 8

Table 2i. Mean TN/TP ratio and TSI based on all the sampling sites in Alachua Sink in 

2004 

Sampling Date TN/TP TSI

02/11/2004 8 55 

05/19/2004 4 63 

06/17/2004 2 69 

07/21/2004 2 73 

08/11/2004 3 56 

09/23/2004 3 77 

Annual mean 4 70*

*

 The values are calculated based on the annual 

average TN, TP, and chla concentrations. The 

value is not a simple mean of the TSI values for 

each sampling event. 

According to Tables 2b and 2c, both TN and TP concentrations were high at the beginning of 

2003 and gradually decreased towards the end of the year. Chla concentrations peaked in May 

with a value of 23.60 μg/L, which is low considering that the TN and TP concentrations during 

the same period were 1.78 mg/L and 0.22 mg/L, respectively. The low mean chla concentration 

(3.96 μg/L) observed by the end of the year could have been caused by shading from the heavy 

growth of floating aquatic plants (JEA, August 2005). 

Except for the October sampling event, TN/TP ratios of all the other sampling events were lower 

than 10, suggesting that the aquatic communities were nitrogen limited. The annual average 

TSI calculated based on the annual average TN and chla concentration is about 66, with 

individual values ranging between 49 and 73. Apparently, the TSI of Alachua Sink is lower 

during wet periods than during dry periods. 

Based on Table 2f, TN concentrations in 2004 started to decline toward summer, and then 

increased sharply in September. A different pattern occurred in the TP measurements; 

concentrations increased after February and remained in the range of 0.6 mg/L to 0.8 mg/L 

throughout the year. Chla concentrations peaked in the summer and declined in August, but 

increased again in September. As in 2003, TN/TP ratios indicated nitrogen limitation and TSI 

values averaged about 66. 
9 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Figure 2. Locations of JEA sampling sites

A total of 11 sites was sampled in 2003 in Alachua Sink. Among these sites, 6 were 

established in Alachua Sink (S1–S6), and 1 was set up in both the inlet and the outlet of 

the sink. Two sites were set up near the control structure. One of them was on the 

Alachua Lake side (AL), and the other was at the mouth of Sweetwater Branch (SWB). 

JEA also sampled the primary sink feature (PSF), which receives the discharge from 

Alachua Sink and discharges into the Floridan aquifer. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 10

Chapter 3: DESCRIPTION OF APPLICABLE WATER 

QUALITY STANDARDS AND CRITERIA 

Alachua Sink is classified as a Class III freshwater body, with a designated use of recreation, 

propagation, and maintenance of a healthy, well-balanced population of fish and wildlife. The 

Class III water quality criterion applicable to the observed impairment is the narrative nutrient 

criterion (in no case shall nutrient concentrations of a body of water be altered so as to cause an 

imbalance in natural populations of aquatic flora or fauna, Subsection 62-302.530(48)(b), 

F.A.C.). 

Because Florida’s current nutrient criterion is narrative only, a nutrient-related target was 

needed to represent levels at which an imbalance in flora or fauna is expected to occur. For 

lakes, the IWR threshold for impairment is based on the TSI and average color (PCUs). As 

Alachua Sink has a mean color greater than 40 PCUs, the IWR threshold for impairment is an 

annual mean TSI of 60, unless paleolimnological information indicates that the natural annual 

average TSI of Alachua Sink was different than 60.

The TSI originally developed by R. E. Carlson (1977) was calculated based on Secchi depth, 

chlorophyll concentration, and total phosphorus concentration, and was used to describe a 

lake’s trophic state. Carlson’s TSI was developed based on the assumption that lakes were all 

phosphorus limited. In Florida, because the local geology produced a phosphorus-rich soil, 

nitrogen can be the sole or co-limiting factor for phytoplankton populations in some lakes. In 

addition, because of the existence of dark-water lakes in the state, using Secchi depth as an 

index to represent lake trophic state can produce misleading results. Therefore, the TSI was 

revised to be based on chla, total nitrogen, and total phosphorus concentrations. The detailed 

calculation of TSI was described in the Northwest Florida District Water Quality 1996 305(b) 

Technical Appendix (Hand et al., 1996). The report also defines the limiting nutrient based on 

the TN/TP ratio. Phytoplankton communities are considered to be limited by nitrogen, 

phosphorus, or both nutrients if the TN/TP ratio is lower than 10, higher than 30, or falls 

between 10 and 30, respectively. 

The Florida-specific TSI was determined based on the analysis of data from 313 Florida lakes. 

The index was adjusted so that a chla concentration of 20 μg/L was equal to a TSI value of 60. 

A TSI of 60 was then set as the threshold for nutrient impairment for most lakes (for those with a 

color higher than 40 PCUs) because generally, phytoplankton may switch to communities 

dominated by blue-green algae at chla levels above 20 μg/L. These blue-green algae are often 

an unfavorable food source for zooplankton and many other aquatic animals. Some blue-green 

algae may even produce toxins that could harm fish and other animals. In addition, the 

excessive growth of phytoplankton and the subsequent death of these algae may consume 

large quantities of dissolved oxygen (DO) and result in anaerobic conditions in lakes, making 

the conditions in an affected lake unfavorable for fish and other wildlife. All of these processes 

may negatively affect the health and balance of native fauna and flora. 

Because of the amazing diversity and productivity of Florida lakes, some lakes have a natural 

background TSI that is different from 60. In recognition of this natural variation, the IWR allows 

for the use of a lower TSI (40) in very clear lakes, a higher TSI if paleolimnological data indicate 
11 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

that a lake was naturally above 60 historically, and the development of site-specific thresholds 

that better represent the levels at which nutrient impairment occurs. For this study, the Florida 

Department of Environmental Protection (Department) used modeling to estimate the natural 

background TSI by setting land uses to natural or forested land, and then compared the 

resulting TSI with the IWR thresholds. After the natural background TSI was determined, an 

increase of 5 TSI units above natural background was used as the water quality target for the 

TMDL. 

Analyses of the current water quality condition of Alachua Sink indicate that the long-term 

annual average TN/TP ratio is less than 10, suggesting that the phytoplankton community of 

Alachua Sink is nitrogen limited. Therefore, TN is the focus of this analysis. The impact of 

changes in TP loading was also estimated to provide a complete view of the nutrient dynamics 

of the watershed. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 12

Chapter 4: ASSESSMENT OF SOURCES 

4.1 Overview of the TMDL Development Process 

While TMDL development is a very complex process, the process used for this TMDL is divided 

into three main steps: 

1. TN and TP loadings from various point and nonpoint sources of pollution to 

Alachua Sink were estimated using the Watershed Management Model (WMM). 

2. Loading estimates from the WMM were entered into the Bathtub eutrophication 

model to establish the relationship between TN and TP loadings and in-lake TN, 

TP, and chla concentrations. The model results for in-lake TN, TP, and chla

were used to calculate the TSI-predicted (TSI-P) for several different loading 

scenarios discussed later. 

3. The loadings to Alachua Sink were adjusted until the TSI-P calculated from the 

model was less than the target TSI. The TN loadings that resulted in achieving 

the target TSI constituted the nutrient TMDL for Alachua Sink.

4.2 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 Alachua Sink 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, agriculture, 

silviculture, and 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 A for 

background information about the state and federal stormwater programs). 

For the purposes of allocating pollutant load reductions required by a TMDL, 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. 

However, the methodologies used to estimate nonpoint source loads do not distinguish between 

NPDES stormwater discharges and non-NPDES stormwater discharges, and as such, this 

section does not make any distinctions between the two. 
13 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

4.3 Estimating TN and TP Loadings Using the WMM 

4.3.1 Breakdown of Sub-basins and Land Uses 

The majority of the surface water flowing into, or occurring in, Paynes Prairie drains through 

Alachua Sink. Alachua Sink receives surface water primarily from three sources: Sweetwater 

Branch, Alachua Lake, and the watershed area directly connecting to Alachua Sink (Figure 3). 

Sweetwater Branch collects surface runoff from the Sweetwater Branch watershed and part of 

the Extension Ditch watershed (UED). 

USWB

LSWB

UED

Sweetwater Branch

Alachua Sink

$+

$+

John R. Kelly Generating Station

Main Street WWTP

Alachua Lake

Prairie Creek

4 2 0 4 Miles

±

.

Figure 3. Delineation of the Paynes Prairie watershed 

The area highlighted in green discharges into Sweetwater Branch, including Upper 

Sweetwater Branch (USWB) and Lower Sweetwater Branch (LSWB); the area highlighted 

in beige discharges into Alachua Lake; and the area highlighted in magenta discharges 

directly into Alachua Sink. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 14

There are two point sources in the watershed: the Main Street Domestic Wastewater Treatment 

Plant (WWTP) (Permit Number FL0027251) and the Gainesville Regional Utilities’ (GRU) John 

R. Kelly Generating Station (Permit Number FL0026646). The Main Street Water Reclamation 

Facility is an advanced secondary activated sludge domestic wastewater treatment facility. The 

facility is permitted to discharge 7.5 mgd annual average daily flow to Sweetwater Branch 

(Table 11). The combined discharge from these facilities turns Sweetwater Branch from an 

intermittently flowing stream into an annual stream (Gottgens and Montague, 1988). 

The John R. Kelly Generating Station is permitted to discharge 0.097 million gallons per day 

(mgd) directly into Sweetwater Branch. The facility discharges cooling tower blowdown and 

low-volume wastewater directly to Sweetwater Branch. Other waste streams, including cooling 

tower overflow, stormwater, pretreated metal cleaning wastes, and boiler blowdown are 

discharged to the municipal stormwater system and then to Sweetwater Branch (Table 12). 

Surface runoff from the area labeled Alachua Lake/Paynes Prairie and highlighted in beige in 

Figure 3 discharges into Alachua Lake. Portions of the water from Newnans Lake, located 

northeast of Paynes Prairie, are diverted into Alachua Lake through a control structure on 

Prairie Creek. A culverted structure controls the flow from Alachua Lake to Alachua Sink. The 

area highlighted in magenta in Figure 3 discharges directly into Alachua Sink. Water 

discharged from Alachua Sink drains to ground water through a sinkhole located in the 

northeast corner of the Alachua Sink watershed. 

For the purpose of calibrating the WMM, the Sweetwater Branch watershed was further divided 

into two sub-basins: Upper Sweetwater Branch (USWB) and Lower Sweetwater Branch 

(LSWB). Another area that discharges into Sweetwater Branch is the Upper Extension Ditch, 

which was designated as the UED sub-basin in this analysis (Figure 3). 

Land use categories in each sub-basin were aggregated using the simplified Level I codes. 

Table 3 lists the acreages of each land use category in areas that discharge directly into 

Alachua Sink, or through either Sweetwater Branch or Alachua Lake. 

Table 3. Classification of land use categories for Alachua Sink (in acres) 

Code Land Use Directly into 

Alachua Sink 

Through 

Sweetwater Branch 

Through 

Alachua 

Lake 

1000 Urban open 0 686 1,384 

Low-density residential 6 133 2,453 

Medium-density residential 0 1,741 1,535 

High-density residential 0 54 505 

2000 Agriculture 1 161 2,837 

3000 Rangeland 0 55 674 

8000 Transportation, communication, and 

utilities 0 94 593 

4000 Forest/rural open 62 522 9,530 

5000/6000 Water/wetland 52 640 15,756 

Total 121 4,087 35,286
15 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

4.3.2 Potential Sources of TN and TP in the Alachua Sink Watershed 

TN and TP loadings into Alachua Sink from the following sources were estimated for the loading 

analysis: 

• Loading through surface runoff, 

• Loading through atmospheric deposition directly into the sink, 

• Loading from point sources that discharge into Sweetwater Branch (John R. Kelly 

Generating Station and Main Street WWTP), and 

• Loading from septic tank leakage. 

4.4 Estimating Watershed Loadings Using the WMM

As noted previously, the WMM was used to estimate TN and TP loading. The Department 

originally funded the development of the WMM model under contract to Camp Dresser and 

McKee (CDM). CDM further refined and developed the model to its present state. WMM is 

designed to estimate the annual or seasonal pollutant loadings from a given watershed and 

evaluate the effect of watershed management strategies on water quality (User’s Manual: 

WMM, 1998). While the strength of the model is its capability to characterize pollutant loadings 

from nonpoint sources, such as stormwater runoff, stream baseflow, and septic tank leakage, 

the model also handles point sources such as discharge from wastewater treatment facilities. 

The estimation of pollution load reduction due to partial or full-scale implementation of on-site or 

regional best management practices (BMPs) is also part of the model’s functions. The 

fundamental assumption of the model is that the stormwater runoff from any given land use is in 

direct proportion to annual rainfall, and is dictated by the portion of the land use category that is 

impervious and the runoff coefficients of both the pervious and impervious areas. 

The governing equation for the model is: 

RL = [Cp + (CI – Cp) IMPL] * I (1) 

Where: 

RL = total average annual surface runoff from land use L (inches/year [in/yr]), 

IMPL = fractional imperviousness of land use L, 

I = long-term average annual precipitation (in/yr), 

CP = pervious area runoff coefficient, and 

CI = impervious area runoff coefficient. 

The model estimates pollutant loadings based on nonpoint pollution loading factors (expressed 

as pounds per acre per year [lbs/ac/yr]) that vary by land use and the percent imperviousness 

associated with each land use. The pollution loading factor ML is computed for each land use, 

L, by the following equation: 

ML = EMCL * RL * K (2) 

Where: 

ML = loading factor for land use L (lbs/ac/year), 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 16

EMCL = Event mean concentration (EMC) of runoff from land use L (mg/L); EMC 

varies by land use and pollutant, 

RL = total average annual surface runoff from land use L computed from 

Equation (1) (in/yr), and 

K = 0.2266, a unit conversion constant. 

Data required for WMM application include: 

• Area of all the land use categories and the area served by septic tanks, 

• Percent impervious area of each land use category, 

• EMC for each pollutant type and land use category, 

• Percent EMC of each pollutant type that is in suspended form, 

• Annual precipitation, and 

• Point source flows and pollutant concentrations.

The calibration of the WMM was conducted on both runoff quantity and quality. This was a twostep procedure, since the water quality calibration is a function of the predicted runoff volumes. 

The calibration of water quantity is usually achieved through adjusting the pervious and 

impervious area runoff coefficients. The typical ranges of runoff coefficients are 0.05 to 0.30 for 

pervious area (User’s Manual: WMM, 1998) and 0.85 to 1.0 for impervious area (Linsley and 

Franziani, 1979). 

After the water quantity calibration, water quality was calibrated by adjusting the pollutant 

delivery ratio—i.e., the percentage of pollutant in the surface runoff that is eventually delivered 

to the destination waterbody. In this analysis, the range of the pollutant delivery ratio was 

estimated using the method developed by Roehl (1962) that correlates the delivery ratio to 

watershed area. 

4.4.1 Estimating Sub-basin Loadings Using the WMM 

As described in the previous section, Alachua Sink receives surface water from Sweetwater 

Branch, Alachua Lake, and the area directly connecting to Alachua Sink. To estimate the 

nutrient load from Sweetwater Branch using the WMM, the model was first set up through 

calibration against the flow data collected at a USGS flow gauging station located on the middle 

reach of the stream (Site Name: Sweetwater Branch at Gainesville, FL, Site ID: 02240988) 

(Figure 4). The Sweetwater Branch watershed was divided into upper and lower sub-basins 

during the analysis (Upper Sweetwater Branch [USWB] and Lower Sweetwater Branch [LSWB]) 

to take advantage of the flow data documented for this gauging station, and model calibration 

was conducted with the data for USWB. 

There were seven full years of daily flow data available for the gauging station (1998–2004). 

The WMM model was calibrated using flow data for 1998, 1999, and 2000, and the calibrated 

model was then used to simulate the flow and TN and TP loadings from 2001 through 2004, 

based on the rainfall and point source discharge data for these years. Because no full-year flow 

data were available for other areas of Paynes Prairie at the time this analysis was conducted, 

the WMM calibration for USWB was applied to all the other sub-basins to simulate surface 

runoff. 

No water quality calibration was conducted for the WMM because of the lack of reliable stream 

water quality data from 1998 through 2002. Model input parameters for TN and TP loading 
17 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

estimation were based on literature values (discussed in a later section). Comparing the TN 

and TP loadings estimated using these model parameters with the TN and TP loading estimates 

obtained by a loading analysis conducted by JEA (Alan Foley, personal communication, 2003) 

indicated a very close match, suggesting that the water quality parameters used in this analysis 

are reasonably accurate. 

To estimate TN and TP loadings into Alachua Sink from Alachua Lake, the discharge from 

Alachua Lake into Alachua Sink and the TN and TP concentrations of the discharge were 

required. However, these data were not available for the period from 2000 through 2002. To 

estimate water quality in Alachua Lake, the WMM model was used to evaluate how the land use 

pattern of the Alachua Lake watershed influences the water quality of Alachua Lake. The WMM 

model (calibrated using the USGS gauging station discussed above) was applied to the entire 

Alachua Lake watershed to estimate the nonpoint flow and TN and TP loadings into Alachua 

Lake. Average TN and TP concentrations of Alachua Lake from 2000 through 2002 were then 

simulated using the calibrated Bathtub model. 

Some preliminary model runs indicated that estimated chla concentrations did not match with 

measured values. After consulting with JEA, the Department found that floating macrophytes 

and aquatic plants heavily covered a significant portion of the Alachua Lake area immediately 

above the Alachua Sink sampling site. Even if phytoplankton can grow normally in other parts 

of Alachua Sink, when water flows through this macrophyte-dominated area, a significant 

portion of the algal biomass is lost due to the shading and filtering effects of the macrophytes. 

This may have resulted in the low chla concentration in the Alachua Lake water that reached the 

control structure. This interpretation is consistent with the findings from JEA’s study that the 

percent phaeophytin in the total chla concentration remained high during all the sampling 

events, indicating that a significant portion of the algal biomass was dead. To adjust for the 

effects of the floating macrophytes, the chla concentration from Alachua Lake was assumed to 

be a constant and was set at the annual mean of the chla concentrations measured by JEA. 

Because of the low discharge through the control structure at the outlet of Alachua Lake from 

2000 through 2002, it was inappropriate to assume that the amount of water discharged into 

Alachua Lake was the same amount of water being conveyed into Alachua Sink. Therefore, for 

model runs over the 2000–02 period, the flow from Alachua Lake to Alachua Sink was obtained 

by calibrating the Bathtub model against the water quality data for Alachua Sink (2000–02). In 

contrast, for the simulations of 2003 and 2004, flows from Alachua Lake to Alachua Sink 

predicted by the Alachua Lake Bathtub model were used as the Bathtub input for Alachua Sink. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 18

USWB

LSWB

UED

Sweetwater Branch

Alachua Sink

$+

$+

John R Kelly Generating Station

Main Street WWTP

Alachua Lake

Prairie Creek

USGS Gauging Station 02240988

. 

4 2 0 4 Miles

±

Figure 4. Location of the USGS gauging station (Site ID: 02240988) used for flow 

calibration 

4.4.2 Data Required for Estimating TN and TP Loadings from Point and Nonpoint 

Sources Using the WMM 

To calibrate the flow estimates of the WMM, the following data were used: 

A. Rain precipitation data from the weather station located at the Gainesville Regional 

Airport (UCAN 3964, COOP 083326) were retrieved from the Climate Interactive Rapid 

Retrieval User System (CIRRUS) hosted by the Southeast Regional Climate Center. 

Table 4 lists annual average precipitation and seasonal variation. The annual average 

precipitation for 1998, 1999, 2000, 2001, 2002, 2003, and 2004 was calculated based on 

the whole-year daily rainfall. 
19 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 4. Annual precipitation at Gainesville Regional Airport, 1998–2004 

Year Annual Precipitation

(in/year) (meters [m]/yr) 

1998 45.62 1.16 

1999 38.34 0.97 

2000 34.39 0.87 

2001 42.14 1.07 

2002 55.33 1.41 

2003 46.62 1.18 

2004 58.33 1.48 

B. The SJRWMD provided daily flow data for the gauging station on Sweetwater Branch 

from 1997 through 2004. This analysis excluded the 1997 data because only random 

measurements were available for each month from January to September, and this was 

not sufficiently accurate for annual flow calculation. The daily flow data for the other 

years (1998–2004) were aggregated into annual flows and listed in Table 5. 

Table 5. Annual stream flow of Sweetwater Branch at USGS Gauging Station 02240988, 

1998–2004 

Year 

Annual Stream Flow 

(acre-feet/year 

[ac-ft/yr]) 

(cubic 

hectometers/year 

[hm3/yr]) 

1998 11,238 13.9 

1999 8,973 11.1 

2000 8,029 9.9 

2001 9,767 12.1 

2002 8,455 10.4 

2003 9,567 11.8 

2004 9,538 11.8 

C. Areas of different land use categories for each sub-basin were obtained by aggregating 

the GIS land use coverage based on the simplified Level I code listed in Table 3. Table 

6 lists the acreage of each land use category for each sub-basin. Table 7 lists the 

percent area that each land use occupies in each sub-basin. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 20

Table 6. Area of each land use category of the watershed that discharges into Alachua 

Sink through Sweetwater Branch 

Land Use Type 

Acreage 

USWB LSWB UED Alachua Sink 

(AS) 

Alachua Lake 

(AL) 

Forest/rural open 136 94 292 62 9,530 

Urban open 608 60 18 0 1,384 

Agriculture 8 9 144 1 2,837 

Low-density residential 25 106 2 6 2,453 

Medium-density residential 808 833 100 0 1,535 

High-density residential 54 0 0 0 505 

Communication and 

transportation 90 5 0 0 593 

Rangeland 5 39 11 0 674 

Water/wetland 87 56 498 52 15,756 

Total 1,820 1,202 1,065 121 35,287

Table 7. Percent area of each land use category in each sub-basin 

Land Use Type 

Percent Area of Each Land Use Category 

USWB LSWB UED AS AL

Forest/rural open 7 8 27 51 27 

Urban open 33 5 2 0 4 

Agriculture < 1 1 14 1 8 

Low-density residential 1 9 0 5 7 

Medium-density residential 44 69 9 0 4 

High-density residential 3 0 0 0 1 

Communication and 

transportation 5 < 1 < 1 0 2 

Rangeland < 1 3 1 0 2 

Water/wetland 5 5 47 43 45 

As shown in Table 7, areas occupied by urban and residential land uses (including low-, 

medium-, and high-density residential areas) appear to be the dominant land uses for the 

USWB and LSWB sub-basins. The total areas of these land use types account for 82% and 

83% of the total watershed area in the USWB and LSWB, respectively. In contrast, in the 

AS and AL sub-basins, which contain more natural land use types, including forest/rural 

open and water/wetland, predominate. The areas occupied by these land use types 

represent 94% and 72% of the total watershed area in the AS and AL sub-basins, 

respectively. 

The watershed area that discharges to Alachua Sink through Sweetwater Branch appears to 

be influenced more by urban and residential land uses than the watershed area discharging 

through Alachua Lake. For the 4,087 acres that discharge into Sweetwater Branch, 2,615 

acres are occupied by urban open and residential land uses, which account for 64% of the 

total watershed area. About 5,878 acres out of 35,286 acres of the watershed discharging 

into Alachua Lake is dominated by urban and residential land uses, which account for about 

17% of total land uses. 
21 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

D. Percent impervious area of each land use category is a very important parameter in 

estimating surface runoff using the WMM. Nonpoint pollution monitoring studies throughout 

the United States over the past 15 years have shown that annual “per acre” discharges of 

urban stormwater pollution are positively related to the amount of imperviousness in a land 

use (User’s Manual: WMM, 1998). Ideally, impervious area is considered as the area that 

does not retain water, and therefore, 100% of the precipitation falling on the impervious area 

should become surface runoff. In practice, however, the runoff coefficient for impervious 

area typically ranges between 95% and 100%. Impervious runoff coefficients lower than this 

range were observed in the literature, but usually this number should not be lower than 80%. 

For pervious area, the runoff coefficient usually ranges between 10% and 20%. However, 

values lower than this range were also observed (User’s Manual: WMM, 1998). In this 

analysis, impervious and pervious runoff coefficients were adjusted to fit model estimates to 

measured data in the process of WMM water quantity calibration. 

It should be noted that the impervious area percentages do not necessarily represent 

directly connected impervious area (DCIA). Using a single-family residence as an example, 

rain falls on rooftops, sidewalks, and driveways. The sum of these areas may represent 

30% of the total lot. However, much of the rain that falls on the roof drains to the grass and 

infiltrates to the ground or runs off the property, and thus does not run directly to the street. 

For the WMM modeling, whenever the area of the watershed that contributes to the surface 

runoff was considered, DCIA was used in place of impervious area. Because local values 

were not available, DCIAs used in this analysis were collected from literature-published 

values or results from other studies (Table 8).

Table 8. Percent directly connected impervious area for different land use categories 

Land Use Categories DCIA Reference 

Forest/rural open 0.5% User’s Manual: WMM, 1998 

Urban open 15.4% User’s Manual: WMM, 1998 

Agriculture 3.7% Brown, 1995 

Low-density residential 27.9% User’s Manual: WMM, 1998 

Medium-density residential 64.2% User’s Manual: WMM, 1998 

High-density residential 79.5% User’s Manual: WMM, 1998 

Communication and transportation 36.20% Brown, 1995 

Rangeland 3.7% CDM 

Water/wetland 30% Harper and Livingston, 1999 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 22

E. Local EMCs of TN and TP for different land use categories were not available and therefore 

were obtained from literature values (Table 9). 

Table 9. EMCs of TN and TP for different land use categories 

Land Use Categories TN

(mg/L) 

TP

(mg/L) Reference 

Forest/rural open 1.25 0.053 Lasi, 1999 

Urban open 1.59 0.220 Lasi, 1999 

Agriculture 2.58 0.465 Lasi, 1999 

Low-density residential 1.77 0.177 Lasi, 1999 

Medium-density residential 2.29 0.300 Lasi, 1999 

High-density residential 2.42 0.490 Lasi, 1999 

Communication and transportation 2.08 0.340 Lasi, 1999 

Rangeland 1.25 0.053 Lasi, 1999 

Water/wetland 1.60 0.189 Lasi, 1999 

The EMCs of TN and TP for most land use categories were cited from a review prepared by 

Harper (1992). The review directly provided the EMCs for agriculture, low-density 

residential, and water/wetland. However, Harper did not directly define the EMCs for urban 

open, medium- and high-density residential, transportation and communication, and 

rangeland. Therefore, some extrapolations were made between the land use categories in 

this analysis and the land use categories defined by Harper. Basically, the urban open area 

was treated as the low-intensity commercial area in Harper’s review. Medium-density 

residential was treated as single-family land use; high-density residential was treated as 

multifamily land use; transportation and communication was treated mainly as highway; and 

rangeland was treated the same as general agriculture. 

F. Not all of the TN and TP transported by stormwater are in the dissolved form. The WMM 

allows the percentage of the total EMC represented by TN and TP attached to suspended 

particles to be defined. This analysis used percent suspended TN and TP values reported 

by Lasi (1999) for the Orange Lake watershed (Table 10). 

Table 10. Percent TP and TN in suspended form for different land use categories 

Land Use Categories TP TN 

Forest/rural open 28% 6% 

Urban open 57% 44% 

Agriculture 38% 20% 

Low-density residential 57% 44% 

Medium-density residential 57% 44% 

High-density residential 57% 44% 

Communication and transportation 57% 44% 

Rangeland 38% 20% 

Water/wetland 48% 77% 

G. The sediment delivery ratio determines how much TN and TP attaching to suspended 

particles will eventually be delivered to the destination waterbody. In this analysis, the range 
23 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

of the sediment delivery ratio was estimated using the correlation between delivery ratio and 

watershed area, developed by Roehl (1962), which is 30%. 

H. To estimate the TN and TP loadings from the leakage of septic tanks, the WMM 

incorporates the concept of a “septic tank failure loading rate,” which defines the percent 

increase of TN and TP loadings from the land use area with septic tank leakage. The range 

of loading increase recommended by the WMM User’s Manual is a 160% to 250% increase 

for TP and a 140% to 200% increase for TN. To provide a margin of safety, this analysis 

adopted the high end of the range in the User’s Manual. 

I. Another value required by the WMM to estimate the influence from leaking septic tanks on 

TN and TP loading is the “septic tank failure rate,” which defines the frequency with which 

septic tanks may fail. Studies conducted on water quality in the Ocklawaha Basin found that 

the annual frequency of septic tank repairs was about 0.97% (Department, 2001). For 

average annual conditions, it is conservative to assume that septic tank system failures 

would be unnoticed or ignored for 5 years before repair or replacement occurred (User’s 

Manual: WMM, 1998). Therefore, the septic tank failure rate used in this analysis was 

calculated by multiplying the repair frequency (0.97%/year) by 5 (years). The result was 

about 5%. 

J. As mentioned previously, there are two point sources in the Upper Sweetwater Branch subbasin: GRU’s John R. Kelly Generating Station (Permit Number: FL0026646) and the Main 

Street WWTP (Permit Number: FL0027251) (Figure 1). GRU provided the annual average 

daily discharge and the TN and TP concentrations of the discharge from the Main Street 

WWTP from 1998 through 2004. Table 11 lists the annual average daily discharge and TN 

and TP concentrations of the discharges calculated on the basis of these data from 1998 

through 2004. 

The discharge permit for the John R. Kelly Generating Station does not require effluent 

monitoring for either TN or TP, and the only available TN and TP concentrations of the 

discharge were from two bioassays conducted by the Department in 1991 and 2002. The 

TN and TP concentrations listed in Table 12 are the mean values from the TN and TP 

concentrations of the two bioassays. 

Table 11. Annual average daily discharge and TN and TP concentrations in the discharge 

from the Main Street WWTP, 1998–2004

Year Daily Discharge

(mgd)

TN

(mg/L)

TP

(mg/L)

1998 7.14 4.12 0.54 

1999 5.36 5.29 0.86 

2000 5.34 4.89 0.53

2001 6.20 5.56 1.06

2002 6.05 4.41 1.07

2003 6.53 4.46 0.77

2004 5.49 3.94 0.53 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 24

Table 12. Estimated annual average daily discharge and effluent TN and TP 

concentrations for the John R. Kelly Generating Station, 1998–2004 

Year Daily Discharge

(mgd) 

TN

(mg/L) 

TP 

(mg/L) 

1998 0.141 2.02 0.910 

1999 0.158 2.02 0.910 

2000 0.119 2.02 0.910 

2001 0.092 2.02 0.910 

2002 0.170 2.02 0.910 

2003 0.102 2.02 0.910 

2004 0.236 2.02 0.910 

4.4.3 WMM Flow Calibration 

The calibration of the WMM on water quantity was primarily conducted by adjusting the runoff 

coefficients for pervious and impervious land use area to fit the estimates to the actual 

measurements. Table 13 lists observations, WMM predictions, errors, and pervious and 

impervious runoff coefficients for the USB. From the table it can be seen that the model 

predicted the measured flows reasonably well. 

Table 13. Results of the WMM dry period water quantity calibration for the USWB, 1998–

2004 

Year 

Measured 

Annual Flow 

(ac-ft/yr) 

Estimated 

Annual Flow 

(ac-ft/yr) 

Pervious Runoff 

Coefficient 

Impervious 

Runoff 

Coefficient 

Percent 

Error 

1998 11,238 11,076 0.10 0.90 -1.4 

1999 8,973 8,614 0.10 0.90 -4.0 

2000 8,029 8,298 0.10 0.90 3.4 

2001 9,767 9,691 0.10 0.90 -0.8 

2002 8,455 10,475 0.10 0.90 23.9 

2003 9,567 10,383 0.10 0.90 8.5 

2004 9,538 10,124 0.10 0.90 6.1 

4.4.4 WMM Flow Simulation 

Keeping all of the model input parameters discussed above the same, the calibrated WMM 

model was then used to simulate surface runoff from all the other sub-basins from 2000 through 

2004, since this represented the period when water quality data for Alachua Sink were available 

(Table 14). 

Table 14. Estimated annual flow (ac-ft/yr) for each sub-basin, 2000–04 

Year USWB LSWB UED AS AL

2000 8,298 1,707 819 73 27,081 

2001 9,691 2,092 1,003 92 33,184 

2002 10,475 2,747 1,318 120 43,571 

2003 10,383 2,314 1,110 101 20,812 

2004 10,124 2,896 1,389 126 45,933 
25 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

4.4.5 WMM TN and TP Loading Estimation 

Using the EMCs, the percentage of nutrients in suspended form, sediment delivery ratio, and 

septic tank failure rate discussed in the previous sections, TN and TP loadings were estimated 

for all the sub-basins from 2000 through 2004 (Table 15). 

Table 15. Predicted TN and TP loadings (pounds per year [lbs/yr]) for each sub-basin, 

2000–04 

Year USWB LSWB UED AS AL

TN TP TN TP TN TP TN TP TN TP

2000 90,248 10,456 8,367 1,238 2,537 370 184 21 81,102 11,842 

2001 117,679 22,105 10,252 1,517 3,109 453 225 26 99,379 14,510 

2002 98,347 22,621 13,461 1,992 4,082 595 296 34 130,485 19,052 

2003 103,004 17,723 11,342 1,678 3,440 502 249 30 109,944 16,053 

2004 84,245 11,987 15,275 2,100 4,304 628 312 38 137,560 20,085 

As shown in Table 15, TN and TP loadings from Upper Sweetwater Branch were always 

important. The only sub-basin that contributed a similar amount of TN and TP to Upper 

Sweetwater Branch was Alachua Lake. However, the lake has a much larger area than Upper 

Sweetwater Branch (Table 6), and a significant portion of the TN and TP loadings from the 

Alachua Lake sub-basin would be attenuated in the lake before being introduced into Alachua 

Sink. Therefore, it is reasonable to say that the water quality of Alachua Sink was most 

significantly influenced by the TN and TP loadings from Upper Sweetwater Branch. 

Tables 16 through 19 list the TN and TP loadings from various point and nonpoint sources. 

Tables 16 through 17 list the TN and TP loadings to Alachua Sink through Sweetwater Branch 

and the area directly connecting to Alachua Sink. Tables 16a–e list the TN loading from various 

point and nonpoint sources in 2000, 2001, 2002, 2003, and 2004, respectively. Tables 17a–e 

list the TP loading from various point and nonpoint sources. Tables 18 through 19 list TN and 

TP loadings into Alachua Lake. 

Table 16a. Contribution of TN (lbs/yr) from different sources in the watershed that 

discharged into Alachua Sink through Sweetwater Branch in 2000 

Land Use Type or Source USWB LSWB UED AS Total Percent

Contribution 

Forest/rural open 131 91 283 60 565 0.6% 

Urban open 1,165 115 35 0 1,315 1.3% 

Agriculture 17 21 323 1 363 0.4% 

Low-density residential 76 327 6 18 565 0.6% 

Medium-density residential 6,125 6,313 756 0 13,195 13.0% 

High-density residential 520 0 0 0 520 0.5% 

Transportation/communication 392 20 0 0 413 0.4% 

Rangeland 6 42 12 0 60 0.1% 

Water/wetland 168 109 969 101 1,347 1.3% 

Septic tank 1,344 1,328 153 4 2,829 2.8% 

Main Street WWTP 79,563 - - - 79,563 78.5% 

J. R. Kelly Generating Station 738 - - - 738 0.7% 

Subtotal 90,248 8,367 2,537 184 101,336 100%
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 26

Table 16b. Contribution of TN (lbs/yr) from different sources in the watershed that 

discharged into Alachua Sink through Sweetwater Branch in 2001 

Land Use Type or Source USWB LSWB UED AS Total Percent

Contribution 

Forest/rural open 161 112 346 74 693 0.5% 

Urban open 1,428 141 43 0 1,612 1.2% 

Agriculture 21 26 396 2 445 0.3% 

Low-density residential 94 401 8 22 525 0.4% 

Medium-density residential 7,506 7,736 927 0 16,168 12.3% 

High-density residential 637 0 0 0 637 0.5% 

Transportation/communication 481 25 0 0 506 0.4% 

Rangeland 7 51 15 0 73 0.1% 

Water/wetland 206 133 1,187 123 1,650 1.3% 

Septic tank 1,647 1,627 187 4 3,466 2.6% 

Main Street WWTP 104,925 - - - 104,925 79.9% 

J. R. Kelly Generating Station 566 - - - 566 0.4% 

Subtotal 117,679 10,252 3,109 225 131,266 100.0%

Table 16c. Contribution of TN (lbs/yr) from different sources in the watershed that 

discharged into Alachua Sink through Sweetwater Branch in 2002 

Land Use Type or Source USWB LSWB UED AS Total Percent

Contribution 

Forest/rural open 211 147 455 97 910 0.8% 

Urban open 1,875 185 57 0 2,116 1.8% 

Agriculture 28 34 520 2 584 0.5% 

Low-density residential 123 527 10 29 689 0.6% 

Medium-density residential 9,855 10,157 1,217 0 21,229 18.3% 

High-density residential 837 0 0 0 837 0.7% 

Transportation/communication 631 33 0 0 664 0.6% 

Rangeland 9 68 20 0 96 0.1% 

Water/wetland 271 175 1,559 162 2,166 1.9% 

Septic tank 2,163 2,137 245 6 4,551 3.9% 

Main Street WWTP 81,298 - - - 81,298 70.0% 

J. R. Kelly Generating Station 1,046 - - - 1,046 0.9% 

Subtotal 98,347 13,461 4,082 296 116,187 100.0%
27 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 16d. Contribution of TN (lbs/yr) from different sources in the watershed that 

discharged into Alachua Sink through Sweetwater Branch in 2003 

Land Use Type or Source USWB LSWB UED AS Total Percent

Contribution 

Forest/rural open 178 124 383 81 766 0.6% 

Urban open 1,580 155 48 0 1,783 1.5% 

Agriculture 23 29 438 2 492 0.4% 

Low-density residential 104 444 9 25 581 0.5% 

Medium-density residential 8,304 8,558 1,025 0 17,887 15.2% 

High-density residential 705 0 0 0 705 0.6% 

Transportation/communication 532 27 0 0 559 0.5% 

Rangeland 8 57 16 0 81 0.1% 

Water/wetland 228 148 1,313 136 1,825 1.5% 

Septic tank 1,823 1,800 207 5 3,835 3.2% 

Main Street WWTP 88,720 - - - 88,720 75.2% 

J. R. Kelly Generating Station 800 - - - 800 0.7% 

Subtotal 103,004 11,342 3,440 249 118,035 100.0%

Table 16e. Contribution of TN (lbs/yr) from different sources in the watershed that 

discharged into Alachua Sink through Sweetwater Branch in 2004 

Land Use Type or Source USWB LSWB UED AS Total Percent

Contribution 

Forest/rural open 223 156 479 102 960 0.9% 

Urban open 1,977 207 60 0 2,243 2.2% 

Agriculture 29 37 548 2 616 0.6% 

Low-density residential 130 598 11 31 770 0.7% 

Medium-density residential 10,390 11,716 1,283 0 23,389 22.5% 

High-density residential 882 0 0 0 882 0.8% 

Transportation/communication 666 37 0 0 703 0.7% 

Rangeland 9 73 21 0 103 0.1% 

Water/wetland 286 199 1,643 171 2,299 2.2% 

Septic tank 2,280 2,253 259 6 4,798 4.6% 

Main Street WWTP 65,922 - - - 65,922 63.3% 

J. R. Kelly Generating Station 1,452 - - - 1,452 1.4% 

Subtotal 84,245 15,275 4,304 312 104,136 100.0%
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 28

Table 17a. Contribution of TP (lbs/yr) from different sources in the watershed that 

discharged into Alachua Sink through Sweetwater Branch in 2000 

Land Use Type or Source USWB LSWB UED AS Total Percent

Contribution 

Forest/rural open 5 3 10 2 20 0.2% 

Urban open 140 14 4 0 158 1.3% 

Agriculture 3 3 50 0 56 0.5% 

Low-density residential 7 28 1 2 37 0.3% 

Medium-density residential 697 718 86 0 1,501 12.4% 

High-density residential 91 0 0 0 91 0.8% 

Transportation/communication 56 3 0 0 59 0.5% 

Rangeland 0 2 0 0 2 0.0% 

Water/wetland 29 19 167 17 232 1.9% 

Septic tank 477 448 52 0 977 8.1% 

Main Street WWTP 8,622 - - - 8,622 71.3% 

J. R. Kelly Generating Station 330 - - - 330 2.7% 

Subtotal 10,456 1,238 370 21 12,086 100.0%

Table 17b. Contribution of TP (lbs/yr) from different sources in the watershed that 

discharged into Alachua Sink through Sweetwater Branch in 2001 

Land Use Type or Source USWB LSWB UED AS Total Percent

Contribution 

Forest/rural open 6 4 12 3 25 0.1% 

Urban open 171 17 5 0 193 0.8% 

Agriculture 3 4 61 0 68 0.3% 

Low-density residential 8 35 1 2 46 0.2% 

Medium-density residential 854 880 105 0 1,840 7.6% 

High-density residential 112 0 0 0 112 0.5% 

Transportation/communication 68 4 0 0 72 0.3% 

Rangeland 0 2 1 0 3 0.0% 

Water/wetland 36 23 205 21 284 1.2% 

Septic tank 585 549 64 1 1,198 5.0% 

Main Street WWTP 20,007 - - - 20,007 83.0% 

J. R. Kelly Generating Station 255 - - - 255 1.1% 

Subtotal 22,105 1,517 453 27 24,103 100.0%
29 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 17c. Contribution of TP (lbs/yr) from different sources in the watershed that 

discharged into Alachua Sink through Sweetwater Branch in 2002 

Land Use Type or Source USWB LSWB UED AS Total Percent

Contribution 

Forest/rural open 8 5 16 3 33 0.1% 

Urban open 225 22 7 0 254 1.0% 

Agriculture 4 5 80 0 90 0.4% 

Low-density residential 11 46 1 3 60 0.2% 

Medium-density residential 1,121 1,156 138 0 2,415 9.6% 

High-density residential 147 0 0 0 147 0.6% 

Transportation/communication 90 5 0 0 94 0.4% 

Rangeland 0 2 1 0 3 0.0% 

Water/wetland 47 30 269 28 373 1.5% 

Septic tank 768 721 84 2 1,573 6.2% 

Main Street WWTP 19,730 - - - 19,730 78.2% 

J. R. Kelly Generating Station 471 - - - 471 1.9% 

Subtotal 22,621 1,992 595 36 25,244 100.0%

Table 17d. Contribution of TP (lbs/yr) from different sources in the watershed that 

discharged into Alachua Sink through Sweetwater Branch in 2003 

Land Use Type or Source USWB LSWB UED AS Total Percent

Contribution 

Forest/rural open 6 4 14 3 27 0.1% 

Urban open 190 19 6 0 214 1.1% 

Agriculture 4 4 67 0 76 0.4% 

Low-density residential 9 39 1 2 50 0.3% 

Medium-density residential 945 974 117 0 2,035 10.2% 

High-density residential 124 0 0 0 124 0.6% 

Transportation/communication 76 4 0 0 79 0.4% 

Rangeland 0 2 1 0 3 0.0% 

Water/wetland 39 25 226 23 315 1.6% 

Septic tank 647 607 70 1 1,326 6.7% 

Main Street WWTP 15,324 - - - 15,324 76.9% 

J. R. Kelly Generating Station 360 - - - 360 1.8% 

Subtotal 17,723 1,678 502 30 19,933 100.0%
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 30

Table 17e. Contribution of TP (lbs/yr) from different sources in the watershed that 

discharged into Alachua Sink through Sweetwater Branch in 2004 

Land Use Type or Source USWB LSWB UED AS Total Percent

Contribution 

Forest/rural open 8 6 17 4 34 0.2% 

Urban open 237 23 7 0 268 1.8% 

Agriculture 4 5 84 0 95 0.6% 

Low-density residential 11 48 1 3 63 0.4% 

Medium-density residential 1,182 1,218 146 0 2,546 17.3% 

High-density residential 155 0 0 0 155 1.1% 

Transportation/communication 95 5 0 0 99 0.7% 

Rangeland 0 3 1 0 4 0.0% 

Water/wetland 49 32 283 29 394 2.7% 

Septic tank 809 760 88 2 1,659 11.2% 

Main Street WWTP 8,782 - - - 8,782 59.5% 

J. R. Kelly Generating Station 654 - - - 654 4.4% 

Subtotal 11,987 2,100 628 38 14,753 100.0%

Table 18a. Contribution of TN (lbs/yr) from different sources in the watershed that 

discharged into Alachua Lake in 2000 

Land Use Type or Source AL Percent

Contribution 

Forest/rural open 9,229 11.4%

Urban open 2,652 3.3% 

Agriculture 6,378 7.9% 

Low-density residential 7,568 9.3% 

Medium- density residential 11,634 14.3% 

High-density residential 4,849 6.0% 

Transportation/communication 2,593 3.2% 

Rangeland 735 0.9% 

Water/wetland 30,653 37.8% 

Septic tank 4810 5.9% 

Prairie Creek 0 0% 

Subtotal 81,102 100%
31 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 18b. Contribution of TN (lbs/yr) from different sources in the watershed that 

discharged into Alachua Lake in 2001 

Land Use Type or Source AL Percent

Contribution 

Forest/rural open 11,309 11.4%

Urban open 3,250 3.3% 

Agriculture 7,816 7.9% 

Low-density residential 9,274 9.3% 

Medium-density residential 14,256 14.3% 

High-density residential 5,942 6.0% 

Transportation/communication 3,178 3.2% 

Rangeland 900 0.9% 

Water/wetland 37,560 37.8% 

Septic tank 5,894 5.9% 

Prairie Creek 0 0% 

Subtotal 99,379 100% 

Table 18c. Contribution of TN (lbs/yr) from different sources in the watershed that 

discharged into Alachua Lake in 2002 

Land Use Type or Source AL Percent

Contribution 

Forest/rural open 14,848 10.9%

Urban open 4,267 3.1% 

Agriculture 10,262 7.5% 

Low-density residential 12,177 8.9% 

Medium-density residential 18,718 13.7% 

High-density residential 7,802 5.7% 

Transportation/communication 4,173 3.1% 

Rangeland 1,182 0.9% 

Water/wetland 49,317 36.2% 

Septic tank 7,739 5.7% 

Prairie Creek 5,716 4.2% 

Subtotal 136,201 100%
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 32

Table 18d. Contribution of TN (lbs/yr) from different sources in the watershed that 

discharged into Alachua Lake in 2003 

Land Use Type or Source AL Percent

Contribution 

Forest/rural open 12,511 4.7%

Urban open 3,596 1.3% 

Agriculture 8,646 3.2% 

Low-density residential 10,260 3.8% 

Medium-density residential 15,772 5.9% 

High-density residential 6,574 2.4% 

Transportation/communication 3,516 1.3% 

Rangeland 996 0.4% 

Water/wetland 41,553 15.5% 

Septic tank 6,521 2.4% 

Prairie Creek 157,444 58.9% 

Subtotal 267,389 100%

Table 18e. Contribution of TN (lbs/yr) from different sources in the watershed that 

discharged into Alachua Lake in 2004 

Land Use Type or Source AL Percent

Contribution 

Forest/rural open 15,653 4.5%

Urban open 4,499 1.3% 

Agriculture 10,818 3.1% 

Low-density residential 12,837 3.7% 

Medium-density residential 19,733 5.6% 

High-density residential 8,225 2.3% 

Transportation/communication 4,399 1.3% 

Rangeland 1,246 0.4% 

Water/wetland 51,991 14.8% 

Septic tank 8,159 2.3% 

Prairie Creek 212,748 60.7% 

Subtotal 350,308 100%
33 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 19a. Contribution of TP (lbs/yr) from different sources in the watershed that 

discharged into Alachua Lake in 2000 

Land Use Type or Source AL Percent

Contribution 

Forest/rural open 331 2.8%

Urban open 318 2.7% 

Agriculture 981 8.3% 

Low-density residential 657 5.5% 

Medium-density residential 1,324 11.2% 

High-density residential 853 7.2% 

Transportation/communication 368 3.1% 

Rangeland 27 0.2% 

Water/wetland 5,283 44.6% 

Septic tank 1,700 14.4% 

Prairie Creek 0 0% 

Subtotal 11,842 100%

Table 19b. Contribution of TP (lbs/yr) from different sources in the watershed that 

discharged into Alachua Lake in 2001 

Land Use Type or Source AL Percent

Contribution 

Forest/rural open 405 2.8%

Urban open 390 2.7% 

Agriculture 1,202 8.3% 

Low-density residential 805 5.5% 

Medium-density residential 1,622 11.2% 

High-density residential 1,045 7.2% 

Transportation/communication 451 3.1% 

Rangeland 33 0.2% 

Water/wetland 6,474 44.6% 

Septic tank 2,083 14.4% 

Prairie Creek 0 0% 

Subtotal 14,510 100%
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 34

Table 19c. Contribution of TP (lbs/yr) from different sources in the watershed that 

discharged into Alachua Lake in 2002 

Land Use Type or Source AL Percent

Contribution 

Forest/rural open 532 2.8%

Urban open 512 2.7% 

Agriculture 1,578 8.3% 

Low-density residential 1,058 5.6% 

Medium-density residential 2,130 11.2% 

High-density residential 1,372 7.2% 

Transportation/communication 592 3.1% 

Rangeland 43 0.2% 

Water/wetland 8,501 44.6% 

Septic tank 2,736 14.4% 

Prairie Creek 236 1.2% 

Subtotal 19,288 100%

Table 19d. Contribution of TP (lbs/yr) from different sources in the watershed that 

discharged into Alachua Lake in 2003 

Land Use Type or Source AL Percent

Contribution 

Forest/rural open 448 1.6% 

Urban open 432 1.6% 

Agriculture 1,329 4.9% 

Low-density residential 891 3.3% 

Medium-density residential 1,794 6.6% 

High-density residential 1,156 4.2% 

Transportation/communication 499 1.8% 

Rangeland 36 0.1% 

Water/wetland 7,162 26.4% 

Septic tank 2,305 8.5% 

Prairie Creek 11,146 41.0% 

Subtotal 27,199 100%
35 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 19e. Contribution of TP (lbs/yr) from different sources in the watershed that 

discharged into Alachua Lake in 2004 

Land Use Type or Source AL Percent

Contribution 

Forest/rural open 561 1.6% 

Urban open 540 1.5% 

Agriculture 1,663 4.7% 

Low-density residential 1,115 3.2% 

Medium-density residential 2,245 6.39% 

High-density residential 1,446 4.1% 

Transportation/communication 624 1.8% 

Rangeland 45 0.1% 

Water/wetland 8,962 25.5% 

Septic tank 2,884 8.2% 

Prairie Creek 15,062 42.8% 

Subtotal 35,147 100%

During the five years from 2000 through 2004, the total TN loadings conveyed through 

Sweetwater Branch and from the area directly connecting to Alachua Sink (including the Upper 

and Lower Sweetwater Branch, Extension Ditch, and Alachua Sink sub-basins) averaged 

114,192 (std. dev. 12,007) lbs/yr (Tables 16a–e). Total TP loadings averaged 19,224 (std. dev. 

5,733) lbs/yr for the same period (Tables 17a–e). 

Of the total TN and TP loadings carried through these sub-basins, TN and TP loadings from the 

Main Street WWTP were the dominant components throughout the period. For TN, the loadings 

contributed by the Main Street WWTP were 79,563, 104,925, 81,298, 88,720, and 65,922 

pounds per year in 2000, 2001, 2002, 2003 and 2004, respectively. This represents 78.5%, 

79.9%, 70.0%, 75.2%, and 63.3% of the total TN loadings to Alachua Sink from its contributing 

watershed (excluding the contribution from Alachua Lake). Surface runoff from the watershed 

(Upper and Lower Sweetwater Branch, Extension Ditch, and Alachua Sink) contributed 21,035, 

25,775, 33,843, 28,615, and 35,763 pounds of TN per year, which represents 21.5%, 20.1%, 

30.0%, 24.8%, and 36.7% of the total TN loading in 2000, 2001, 2002, 2003, and 2004, 

respectively. 

For TP, the loadings contributed by the Main Street WWTP were 8,622, 20,007, 19,730, 15,324, 

and 8,782 pounds per year in 2000, 2001, 2002, 2003, and 2004, respectively. These loads 

represent 71.3%, 83.0%, 78.2%, 76.9%, and 59.5% of the total TP loadings carried through 

Sweetwater Branch in this period (2000–04). Surface runoff from the watershed (including 

Upper and Lower Sweetwater Branch, Extension Ditch, and Alachua Sink) contributed 3,134, 

3,841, 5,943, 4,249, and 5,317 pounds of TP per year over the same period, which represents 

about 28.7%, 17.0%, 21.8%, 13.1%, and 40.5% of the total TP loading. 

Both TN and TP loadings from nonpoint sources from the Sweetwater Branch watershed 

predicted by this analysis are close to the loading estimates from a study conducted by JEA 

(1999–2001). The years of overlap between the studies are 2000 and 2001. JEA’s estimate of 

the nonpoint source TN loading was about 21,966 pounds per year compared with 23,405 

pounds per year in this analysis (an average of years 2000 and 2001), and JEA’s nonpoint 

source TP loading was about 3,614 pounds per year compared with 3,488 pounds per year in 

this analysis (an average of years 2000 and 2001). 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 36

TN and TP loadings from the other point source, the John R. Kelly Generating Station, are 

relatively insignificant and represent less than 2% of the total TN and TP loadings carried 

through Sweetwater Branch in the period of this analysis. 

Among the nonpoint sources that discharge into Sweetwater Branch and in the area directly 

connected to Alachua Sink, urban and residential land uses appear to dominate the percent 

contribution of TN and TP loadings (Tables 16 and 17). These results indicate that the TN and 

TP loadings in Sweetwater Branch and from the area directly connected to Alachua Sink are 

highly influenced by human activities. 

No point sources were identified in the watershed area that discharges into Alachua Lake. The 

largest contributors of TN and TP in this sub-basin are forest/rural open and water/wetland. 

Among the total loading from the sub-basin, about 49.2% of the TN and 47.2% of the TP came 

from forest/rural open and water/wetland land uses from 2000 through 2002 (and natural 

background wet and dry cases). Prairie Creek can represent a large source of TN and TP into 

Alachua Lake. Based on model simulations for 2003 and 2004, Prairie Creek contributed about 

35% of the TP load to Alachua Lake and nearly 60% of the TN input. Note that in the absence 

of actual gauged inflow data, simulations for both years assumed that 41% of the annual Prairie 

Creek flow went to Paynes Prairie. 

The majority of the TN and TP loading contributed by human land use types comes from urban 

and residential land uses (Tables 18 and 19). 
37 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Chapter 5: Determination of Assimilative Capacity 

5.1 Lake Modeling Using the Bathtub Model 

5.1.1 Bathtub Eutrophication Model 

The Bathtub eutrophication model is a suite of empirically derived, steady-state models 

developed by the U. S. Army Corps of Engineers (USACOE) Waterways Experimental Station. 

The primary function of these models is to estimate nutrient concentrations and algal biomass 

resulting from different patterns of nutrient loadings. The procedures for selection of the 

appropriate model for a particular lake are described in the User’s Manual. The empirical 

prediction of lake eutrophication using this approach typically can be described as a two-stage 

procedure using the following two categories of models (Walker, 1999): 

• The nutrient balance model relates in-lake nutrient concentration to external nutrient 

loadings, morphometry, and hydrology. 

• The eutrophication response model describes relationships among eutrophication 

indicators within the modeled lake, including nutrient levels, chla, transparency, and 

hypolimnetic oxygen depletion. 

Figure 5 describes the conceptual scheme used by Bathtub to relate the external loading of 

nutrients to in-lake nutrient concentrations, and the physical, chemical, and biological response 

of Alachua Sink to the level of nutrients. 

The nutrient balance model adopted by Bathtub assumes that the net accumulation of nutrients 

in a lake is the difference between nutrient loadings into the lake from various sources and the 

nutrients carried out through outflow and the losses of nutrients through whatever decay 

process occurs inside the lake. The net accumulation in the lake is calculated using the 

following equation: 

Net accumulation = Inflow – Outflow – Decay (3) 

Loading of nutrients 

 (Flow and concentration) 

 

 Physical characteristics of Alachua Sink In-lake nutrient Chla, Secchi depth, 

(Surface area and mean depth) concentrations (TN & TP) DO 

Hydraulic characteristics of Alachua Sink 

 (Water residence time) 

Figure 5. Bathtub conceptual scheme 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 38

Equation (3) is solved by assuming that the pollutant dynamics in the lake are at a steady state, 

i.e., the net accumulation of the pollutant in the lake equals zero. 

In this study, “inflow” included TN and TP loadings through surface stormwater runoff from 

various land use categories, point sources, the leakage of septic tanks, and atmospheric 

deposition (bulk) directly on the surface of Alachua Sink. To address nutrient decay in Alachua 

Sink, Bathtub provided several alternatives, depending on the inorganic/organic nutrient 

partitioning coefficient and reaction kinetics. The major pathway of decay for TN and TP in the 

model is through sedimentation to the bottom of Alachua Sink. 

Prediction of the eutrophication response by Bathtub also involves choosing one of several 

alternative models, depending on whether the algal communities are limited by phosphorus or 

nitrogen, or co-limited by both nutrients. The suite of models also contains scenarios that 

include algal communities limited by light intensity or controlled by the Alachua Sink flushing 

rate. In addition, the response of chla concentration to the in-lake nutrient level is characterized 

by two different kinetic processes: linear or exponential. The variety of models available in 

Bathtub allows the user to choose specific models based on the particular condition of the 

project lake. Section 5 discusses the specific Bathtub models used in this analysis. 

One feature offered by Bathtub is the “calibration factor.” The empirical models implemented in 

Bathtub are mathematical generalizations about lake behavior. When applied to data from a 

particular lake, measured data may differ from predictions by a factor of two or more. Such 

differences reflect data limitations (measurement or estimation errors in the average inflow and 

outflow concentrations), the unique features of a particular lake (Walker, 1999), and unexpected 

processes inherent to a lake such as Alachua Sink. The calibration factor offered by Bathtub 

provides model users with a method to calibrate the magnitude of lake response predicted by 

the empirical models. The model calibrated to current conditions (against measured data from 

Alachua Sink) can then be applied to predict changes in lake conditions likely to result from 

specific management scenarios, under the condition that the calibration factor remains constant 

for all prediction scenarios. 

5.1.2 Data Requirements for Running Bathtub 

Data requirements for the Bathtub model include the following: 

• Physical characteristics of Alachua Sink (surface area, mean depth, length, and mixed 

layer depth), 

• Meteorological data (precipitation and evaporation retrieved from CIRRUS), 

• Measured water quality data (TN, TP, and chla concentrations of Alachua Sink water, 

TN and TP concentrations in precipitation, etc.), 

• Loading data (flow and TN and TP concentrations of the flow from various point and 

nonpoint sources of pollution), and 

• Coefficient of variance (CV) of all the measured data. 
39 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

5.1.3 Calculation of the Trophic State Index 

TSI values were calculated using the procedures outlined in Florida’s 1996 305(b) report: 

TSI = (CHLATSI + NUTRTSI)/2 (4) 

Where: 

CHLATSI = 16.8 + 14.4 × LN (CHLA)] 

TNTSI = 56 + [19.8 × LN(TN)] 

TN2TSI = 10 × [5.96 + 2.15 × LN(TN + 0.0001)] 

TPTSI = [18.6 × LN(TP × 1000)] –18.4 

TP2TS = 10 × [2.36 × LN(TP × 1000) – 2.38] 

The procedure addresses limiting nutrient considerations by calculating NUTRTSI: 

If TN/TP > 30 then NUTRTSI = TP2TSI

If TN/TP < 10 then NUTRTSI = TN2TSI 

If 10 < TN/TP < 30 then NUTRTSI = (TPTSI + TNTSI)/2 

5.2 TMDL Scenario Development for Alachua Sink 

Once the WMM and Bathtub model calibrations were achieved (described in the next section), 

the TMDL for Alachua Sink was developed by evaluating the TSIs representative of both a dry 

period and a wet period for each of the following scenarios: 

A. The TSI for the current condition. 

B. The TSI after the DCIA and EMC of runoff from all the human land use categories (urban 

open; low-, medium-, and high-density residential; agriculture and rangeland; and 

transportation, communication, and utilities) were improved to the level of natural land 

(forest/ rural open), and the point source contributions were reduced to current annual 

average flow and given the concentration of the EMC for forest/rural open. 

C. The TSI after the DCIA and EMC of runoff from all the human land use categories (urban 

open; low-, medium-, and high-density residential; agriculture and rangeland; and 

transportation, communication, and utilities) were improved to the level of natural land 

(forest/rural open) and the point source contributions were totally removed. 

Scenario C was considered the natural background condition of Alachua Sink. The TN and TP 

loadings that result in a TSI of 60 would typically be considered as the TMDL for Alachua Sink. 

However, if the TSI for Scenario C were different from 60, the TSI for Scenario C plus 5 TSI 

units would become the new target TSI threshold for Alachua Sink. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 40

5.3 Establishing the Relationship between TN and TP Loading to Alachua 

Sink and In-lake Concentrations 

5.3.1 Atmospheric Loading of TN and TP into Alachua Sink and Alachua Lake 

One source of TN and TP loading to Alachua Sink and Alachua Lake that the WMM did not was 

TN and TP falling directly onto the surface of these waterbodies. In this analysis, the 

atmospheric loading of TN and TP was calculated by multiplying the amount of precipitation 

directly falling on Alachua Sink (calculated by multiplying the annual precipitation by the surface 

area of Alachua Sink) by the TN and TP concentration of the rainfall. Because no data for the 

TN and TP concentration of rainfall were available for the area, published values were used; 

these were 0.1 mg/L and 0.05 mg/L for TN and TP, respectively (Stites et al., 2001). Table 20

tabulates the calculated annual TN and TP loadings from atmospheric loading. 

Table 20. Atmospheric loading of TN and TP (lbs/yr) into Alachua Lake and Alachua 

Sink, 2000–04 

Year Into Alachua Sink Into Alachua Lake 

TN TP TN TP

2000 10 5 2,373 1,187 

2001 12 6 2,909 1,454 

2002 17 8 3,820 1,910 

2003 16 8 5,114 2,538 

2004 16 8 4,990 2,495 

5.3.2 Simulated TN, TP, and Chla Concentrations in Alachua Lake Using the 

Bathtub Model 

Another source of TN and TP loadings into Alachua Sink is the loadings from Alachua Lake. 

Because no flow and water quality data were available from 2000 through 2002, the Bathtub 

model after calibration was used to simulate annual average TN and TP concentrations of 

Alachua Lake, using the TN and TP concentrations measured by JEA in 2003. Because a 

significant portion of the channel that conveys Alachua Lake water into Alachua Sink may be 

covered by floating macrophytes and aquatic plants—which limit the growth of phytoplankton in 

the covered area by blocking light and serve as a filter system that removes the biomass of 

phytoplankton grown in other areas of Alachua Lake—using the model-simulated chla 

concentration as the algal biomass input from Alachua Lake to Alachua Sink may not match well 

with measured levels. Therefore, the chla concentration of the outlet water from Alachua Lake 

was based on measurements by JEA and the ACEPD in 2003 and 2004. 

5.3.3 Data Required for the Simulation of TN and TP Concentrations in Alachua 

Lake 

This section describes how the data required to simulate the TN and TP concentrations for 

Alachua Lake were developed. It should be noted that the physical characteristics data listed in 

Table 21 for Alachua Lake from 2000 through 2004 are not based on measured results. No 

measured data on lake characteristics were available from 2000 through 2004. The following 

procedures were used to calculate the surface area and mean depth of Alachua Lake: 

1. Jim Weimer (personal communication), Paynes Prairie Park biologist, provided a 

spreadsheet of prairie water levels from 1976 through 1999. Annual average water 
41 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

levels were calculated from the spreadsheet. In addition, annual average flows for 

Prairie Creek from 1979 through 1999 were calculated from daily gauge records. 

2. A regression equation was developed for the relationship between the annual average 

Prairie Creek flow (cubic feet per second [cfs]) and annual prairie water surface 

elevation: 

Alachua Lake surface elevation = 0.030 * annual average Prairie Creek flow + 53.61 

(r2

 = 0.39, significant at α = 0.05) 

3. Alachua Lake surface elevations from 2000 through 2004 were calculated based on the 

above equation and the elevation data provided by JEA as part of sampling efforts in 

2003 and 2004. 

4. Alachua Lake surface area and lake volume from 2000 through 2004 were estimated 

using Alachua Lake characteristic curves developed by the SJRWMD for Paynes Prairie 

(Robison, 1997) (see Appendix B). 

5. The mean depth of Alachua Sink was calculated by dividing the volume of Alachua Sink 

by the surface area of Alachua Sink. 

6. Because Alachua Lake is shallow, the mixed layer depth was assumed to be equal to 

the mean depth of Alachua Lake. 

7. Annual evaporation rates were only available for Gainesville through 2000. Rates for 

2001 through 2004 were based on a regression relationship between the Gainesville and 

Lake City sites: 

Annual evaporation (inches) = 32.83 + 0.405*Lake City 

(r2

 = 0.44, significant at α = 0.05) 

Estimating lake physical characteristics using these procedures results in additional 

uncertainties, because the regression equation developed may not totally match the current 

situation of Alachua Sink or incorporate other factors such as prolonged drought conditions. 

Tables 21 through 23 list the data used for the model simulation. 

Table 21. Physical characteristics of Alachua Lake, 2000–04 

Year Lake Surface Area 

(square kilometers [km2]) 

Mean Depth 

(m) 

Mixed Layer Depth 

(m) 

2000 12.33 0.385 0.385 

2001 12.33 0.385 0.385 

2002 12.33 0.385 0.385 

2003 28.78 0.57 0.57 

2004 15.28 0.60 0.60 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 42

Table 22. Precipitation and evaporation (m/yr), 2000–04 

Year Precipitation Evaporation

2000 0.87 1.66 

2001 1.07 1.48 

2002 1.41 1.48 

2003 1.18 1.65 

2004 1.48 1.48 

Table 23. Alachua Lake flow and the TN and TP concentrations of different sources in 

2003 

Land Use Type or Source Flow 

(hm3/yr) 

TN 

(mg/L) 

TP 

(mg/L) 

Forest/rural open 4.75 1.19 0.04 

Urban open 1.48 1.10 0.13 

Agricultural 1.76 2.23 0.34 

Low-density residential 3.8 1.22 0.11 

Medium-density residential 4.52 1.58 0.18 

High-density residential 1.78 1.67 0.29 

Transportation, communications, and utilities 1.11 1.44 0.20 

Rangeland 0.42 1.08 0.04 

Water/wetland 25.68 0.73 0.13 

Prairie Creek 31.6 2.26 0.16 

Notes: 

a

 Bathtub does not allow the direct input of loading. Therefore, the data presented here are flow and the TN and TP concentrations 

of the flow. 

b

 The TN and TP concentrations presented for each source were calculated by dividing the TN and TP loadings from the entire 

watershed by the total flow associated with each source. 

c Based on the results of a TMDL study conducted on Newnans Lake, Prairie Creek diverts about 41% of the outflow from Newnans 

Lake into Paynes Prairie (Gao and Gilbert, 2003). Carol Lippincott (personal communication) from the SJRWMD provided TN 

concentrations of canals for 2003 and 2004. The TP concentrations used for Prairie Creek were the average over the period from

2000 through 2002. 

5.3.4 Calibrating Bathtub Using the TN and TP Concentrations of Alachua Lake 

Measured in 2003 

Table 24 lists the TN and TP concentrations measured by JEA in 2003 (data on 11/05/03 were 

from the ACEPD). However, only TN and TP concentrations from the sampling trips of May 22 

and June 9 were used to calibrate the model because, as described subsequently, Alachua 

Lake was not at a steady-state condition before and after these dates. Data from other 

sampling periods were not used because Bathtub is a steady-state model, and the modeling 

requires that the target waterbody be as close to the steady state as possible. 
43 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 24. TN and TP concentrations of Alachua Lake in 2003 (all values in mg/L) 

Sampling Events TN TP

02/12/03 2.739 1.11 

03/12/03 2.840 1.17 

03/27/03 2.290 0.62 

05/07/03 2.130 0.38 

05/22/03 1.880 0.14 

06/09/03 1.921 0.13 

10/16/03 1.170 0.01 

11/05/03 0.980 0.10 

12/09/03 1.500 0.03 

Figure 6 shows the load of TN and TP in the water column of Alachua Lake over the sampling 

period in 2003. The load of water column TN and TP was relatively low in February because of 

the small lake volume at the time. The amount of TN and TP decreased significantly from 

March to late May, and stayed relatively constant in the late May and early June sampling 

events. By June, the water column TN decreased by about 13 tons and reduced to about 77% 

of the water column TN in February. The phosphorus decrease was even more dramatic. By 

June, the water column phosphorus decreased by about 20 tons and reduced to about 13% of 

the water column TP in February. 

0.00

10.00

20.00

30.00

40.00

50.00

60.00

Feb. 12 Mar. 12 Mar. 27 May. 7 May. 22 Jun. 9 Oct. 16 Dec. 9

Sampling Time

Amount in the lake (tons)

50.00

51.00

52.00

53.00

54.00

55.00

56.00

57.00

Lake Elevation (ft)

TN

TP

Lake elevation

Figure 6. TN and TP Load in Alachua Lake in 2003 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 44

One explanation for the dramatic increase in water column TN and TP observed at the 

beginning of the year and the subsequent gradual decrease is that Alachua Lake was not at a 

steady state throughout 2003. Alachua Sink went through several dry years before 2003, and a 

significant portion of the lake bottom was exposed to the air. This process may have caused 

the organic materials containing nitrogen and phosphorus to be oxidized. When Alachua Lake 

was reflooded in early 2003, oxidized nitrogen and phosphorus-containing materials, which are 

more soluble than the original organic materials in the sediment, would have been released into 

the water column and would have resulted in the high water column TN and TP concentrations 

when the lake reached its highest level in March (Wetzel, 2001). However, the high water 

column TN and TP content created through this internal recycling process is usually not stable 

over an extended period, and water column TN and TP content usually decreases through 

sedimentation. The subsequent sedimentation of TN and TP may have caused the decrease of 

the water column TN and TP since March. 

Further decreases of TN and TP concentrations were observed during the October sampling 

event, and the concentrations increased slightly during the December sampling event. The TP 

concentration was below the detection limit during the October sampling event, which is not very 

common for central Florida lakes. Based on communications with JEA and the park biologist 

who has been constantly surveying Alachua Sink’s condition, the Department found that floating 

aquatic plants, including water hyacinth, duck weed, salvinia, and water lettuce, developed 

heavily after June. Alachua Lake was almost entirely covered by floating aquatic plants during 

the October sampling event. A significant portion of the surfaces of both Alachua Lake and 

Alachua Sink remained covered by these plants during the December sampling event. Nutrient 

uptake by these aquatic plants could have contributed significantly to the low TN and TP 

concentration observed in the October and December sampling events. 

It should be noted that if the TN and TP were taken up by phytoplankton, it would remain in the 

water column and be included in surface water samples. In contrast, surface water samples 

would not include that portion of TN and TP that is fixed by floating aquatic plants. Therefore, 

the October TN and TP concentrations were considered underestimates of the actual TN and 

TP concentrations of Alachua Lake and Alachua Sink, because the data were collected when 

both waterbodies were heavily influenced by floating aquatic plants. 

Based on the discussion above, the Department believes that it would be inappropriate to 

calibrate the Bathtub model using all the TN and TP data measured in 2003. Only the TN and 

TP concentrations measured in the sampling events of May 22 and June 9 were used for the 

model calibration, because during this period, Alachua Sink reached a relatively stable condition 

and was still not heavily influenced by the colonization of floating aquatic plants. 

To calibrate the Bathtub model, each source of TN and TP was designated as an independent 

tributary. Flow and the TN and TP concentration from leaking septic tanks are not defined in 

Table 23 because in Bathtub, septic tank loading is characterized differently from other point 

and nonpoint sources. Instead of being defined by flow and the pollutant concentration of the 

flow, septic tank loading is defined by the flux of TN and TP into Alachua Sink and is calculated 

by dividing the septic tank TN and TP loadings by the surface area of Alachua Sink. In this 

analysis, annual average septic tank loads to Alachua Lake in 2003 were 6,521 pounds per year 

for TN and 2,305 pounds per year for TP. The annual average surface area of Alachua Lake for 

2003 was 28.78 square kilometers (km2

). Utilizing appropriate conversion units and dividing the 

loading by the surface area yields an average flux of 0.282 milligrams per square meter per day 

(mg/m2

/day) for TN and 0.099 mg/m2/day for TP. 
45 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Bathtub provides several alternative submodels for estimating the influence of sedimentation on 

the in-lake TN and TP concentrations. In this analysis, the settling velocity submodel was 

chosen for both TN and TP calculations. This submodel assumes that the sedimentation of TN 

and TP is in first-order kinetics and should linearly correlate with in-lake TN and TP 

concentrations. The submodel also assumes that the depth of Alachua Sink influences 

sedimentation—i.e., the deeper Alachua Sink is, the slower the sedimentation. The submodel fit 

the conditions for Alachua Lake because the lake is relatively shallow and large in surface area. 

Continued wind mixing prevents the lake from forming thermal stratification, which would 

otherwise prevent the particles from being resuspended once they settled to the bottom. 

Continued wind mixing through the entire water column also reduces the particle-settling rate by 

continuously bringing the settled particles back into the water column. These processes 

produce a relatively low settling rate in Alachua Lake. 

Other sedimentation submodels provided by Bathtub assume second-order kinetics, which fit 

reasonably well with lakes that form thermal stratification during the summer. However, these 

models would overestimate the sedimentation of Alachua Lake, and in turn cause the 

underestimation of in-lake TN and TP concentrations. 

Table 25 shows the measured and Bathtub-predicted TN and TP concentrations for Alachua 

Lake. The relative percentage error is based on a comparison between the measured average 

for May through June (discussed in the text) and the annual mean predicted by the model. In 

the case of TN, the annual mean and median based on measurements are very similar to the 

model prediction.

Table 25. Bathtub calibration for Alachua Lake in 2003) 

Mean/Median for year Measured

May–June Bathtub Predicted Error 

TN (mg/L) 1.941/1.92 1.901 1.945 2.3% 

TP (mg/L) 0.41/0.14 0.140 0.152 8.6% 

5.3.5 Simulation of TN and TP concentrations of Alachua Lake for 2004 

As discussed earlier, JEA conducted three additional surveys in 2004. The ACEPD also 

sampled Sweetwater Branch, Alachua Lake, and Alachua Sink in 2004. Tables 26 and 27 

summarize Alachua Lake flow and TN and TP concentrations in 2004 and sampling results in 

2004, respectively. A simulation of the Bathtub model was completed for 2004, and Table 28

presents the results. Measurements over the January through September period were 

averaged and compared with the annual average predicted by Bathtub. The model 

underpredicted both the TN and TP in 2004. 

A few factors could be contributing to the underpredictions. First, note that the last sampling 

event for Alachua Lake occurred on September 23, 2004 (both JEA and Alachua County), and 

reported concentrations for both TN and TP were the highest of the year. If measurements for 

the two common sampling dates are averaged (5/19 and 9/23) to yield a single measurement 

for each date, the observed average for TN and TP becomes 2.092 mg/L and 0.195 mg/L, 

respectively, and the respective errors are reduced to -22.6% and 22.0%, respectively. 

Second, in 2004 there were only about half the elevation measurements compared with the 

number in 2003. The available elevations in 2004 indicated greater fluctuations in both Alachua 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 46

Lake and Alachua Sink compared with 2003. Elevations were used to estimate the surface 

area, storage volume, and ultimately, in-lake concentrations and discharge. Third, inflow from 

Prairie Creek was a major contributor of TN and TP loading to Alachua Lake, and due to limited 

water quality information, similar concentrations were assumed for both 2003 and 2004. 

Table 26. Alachua Lake flow and TN and TP concentrations of different sources in 2004 

Land Use Type or Source Flow 

(hm3/yr) 

TN 

(mg/L) 

TP 

(mg/L) 

Forest/rural open 5.94 1.19 0.04 

Urban open 1.85 1.10 0.13 

Agricultural 2.21 2.23 0.34 

Low-density residential 4.76 1.22 0.11 

Medium-density residential 5.65 1.58 0.18 

High-density residential 2.23 1.67 0.29 

Transportation, communications, and utilities 1.39 1.44 0.20 

Rangeland 0.52 1.08 0.04 

Water/wetland 32.13 0.73 0.13 

Prairie Creek 42.7 2.26 0.16 

Notes: 

a

 Bathtub does not allow the direct input of loading. Therefore, the data presented here are flow and TN and TP concentrations of 

the flow. 

b

 TN and TP concentrations presented for each source were calculated by dividing the TN and TP loadings from the entire 

watershed by the total flow created in the watershed. 

c

 Based on the results of a TMDL study conducted on Newnans Lake, Prairie Creek diverts about 41% of the outflow from Newnans 

Lake into Paynes Prairie (Gao and Gilbert, 2003). Carol Lippincott (personal communication) from the SJRWMD provided TN 

concentrations of canals for 2003 and 2004. The TP concentrations used for Prairie Creek were the average over the period from

2000 through 2002. 

Table 27. TN and TP concentrations of Alachua Lake in 2004 (all values in mg/L) 

Sampling Events TN TP

01/15/2004 1.50 0.1 

02/11/2004 2.18 0.09 

03/10/2004 2.10 0.21 

04/14/2004 2.40 0.1 

05/19/2004 1.69 0.12 

05/19/2004 2.00 0.098 

06/17/2004 1.60 0.2 

07/21/2004 2.1 0.14 

08/11/2004 2.2 0.1 

09/23/2004 2.96 0.62 

09/23/2004 2.85 0.81 

Table 28. Bathtub calibration for Alachua Lake in 2004 

Mean/Median for year Bathtub Predicted Error

TN (mg/L) 2.144/2.18 1.619 -24% 

TP (mg/L) 0.237/0.12 0.152 -36% 
47 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

5.3.6 Simulation of TN and TP concentrations of Alachua Lake from 2000 through 

2002 

To estimate the water quality condition of dry years, the calibrated Bathtub model was used to 

simulate the TN and TP concentrations of Alachua Lake from 2000 through 2002. The physical 

characteristics of the lake, and precipitation in to and evaporation out of Alachua Lake, used for 

simulation were the mean values calculated based on the annual average values of 2000 

through 2002 (listed in Tables 21 and 22). Table 29 lists the flow from different sources and the 

TN and TP concentrations of the flow used for the model simulation. These values are also the 

mean values calculated based on the values for 2000, 2001, and 2002. The method used to 

calculate these values is described in the note to Table 23. Table 30 lists the simulated TN and 

TP concentrations for Alachua Lake from 2000 through 2002. 

Table 29. Alachua Lake flow, and TN and TP concentrations of different sources, 2000–

02 

Land Use Type or Source Flow 

(hm3/yr) 

TN 

(mg/L) 

TP 

(mg/L) 

Forest/rural open 4.48 1.19 0.04 

Urban open 1.40 1.10 0.13 

Agricultural 1.66 2.23 0.34 

Low-density residential 3.58 1.22 0.11 

Medium-density residential 4.26 1.58 0.18 

High-density residential 1.68 1.67 0.29 

Transportation, communications, and utilities 1.05 1.44 0.20 

Rangeland 0.40 1.08 0.04 

Water/wetland 24.21 0.73 0.13 

Prairie Creek 0.22 3.87 0.16 

Table 30. Bathtub-simulated TN and TP concentrations of Alachua Lake, 2000–02 

Year Simulated TN 

(mg/L) 

TP 

(mg/L) 

2000 1.534 0.157 

2001 1.384 0.155 

2002 1.188 0.143 

Composite of 2000–02 1.340 0.156 

5.4 Bathtub Calibration for the Alachua Sink Model 

5.3.1 Data Required for Calibrating the Bathtub Model for Alachua Sink 

The relationship between TN and TP loading and the in-lake TN and TP concentrations in 

Alachua Sink were established by fitting the Bathtub model predictions for Alachua Sink with the 

measured TN and TP concentrations for Alachua Sink. No flow measurements were available 

from Alachua Lake to Alachua Sink from 2000 through 2002. Because of the control structure 

located in the channel from Alachua Lake to Alachua Sink, it is also difficult to model the flow 

using Bathtub. Flow data were available for the year 2003. Therefore, two Bathtub calibrations 

were conducted. For the period from 2000 through 2002, Bathtub calibration used flow and TN 

and TP concentrations of the flow from various point and nonpoint sources estimated using the 

WMM. Based on discussions with area experts, it is the Department’s understanding that there 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 48

was little or no discharge from Alachua Lake from 2000 through 2002. Annual rainfall totals for 

1999 through 2001 were between 3 and 9 inches below normal each year (a 3-year deficit of 

20.2 inches), and 2002 ended approximately 4 inches above normal. Consequently, a minimal 

annual discharge of 1 hm3

 from Alachua Lake was assumed for 2000 through 2002. For 2003 

and 2004, the measured flow from Alachua Lake to Alachua Sink was used together with the 

flows from all the other point and nonpoint sources (established using the WMM) to calibrate the 

Bathtub model. 

The data used for the Bathtub calibration for Alachua Sink from 2000 through 2002 were the 

mean annual averages calculated from the values for each year from 2000 through 2002. The 

model calibration for 2003 and 2004 only used data from those respective years. Tables 31

through 38 list the data required for model calibration. 

Table 31. Physical characteristics of Alachua Sink, 2000-–04 

Year Lake Surface Area 

(km2) 

Mean Depth 

(m) 

Mixed Layer Depth 

(m) 

2000 0.02 0.78 0.78 

2001 0.02 0.82 0.82 

2002 0.02 0.85 0.85 

Mean 0.02 0.82 0.82 

2003 0.062 1.94 1.94 

2004 0.048 1.50 1.50 

For 2003 and 2004, the surface area and volume of Alachua Sink were determined based on 

the water surface elevation (Table 32) and the bathymetry data (Table 33) provided to the 

Department by GRU and JEA. Because no measured surface elevation was available from 

2000 through 2002, a correlation was developed between the surface elevation and the total 

flow into Alachua Sink, using the surface elevations and flows measured in 2003 (Figure 7). 

The WMM-predicted average annual flow from 2000 through 2002 was then used with this 

correlation to estimate the surface elevation of Alachua Sink from 2000 through 2002. The 

volume and surface area of Alachua Sink during this period was then estimated using the 

bathymetry data provided in Table 33. The mean depth of Alachua Sink was calculated by 

dividing the volume of Alachua Sink by the surface area of Alachua Sink. Due to the 

shallowness of Alachua Sink, the mixed layer depth was assumed to be equal to the mean 

depth (Table 31).
49 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

y = 2E-07x + 40.469

R2

 = 0.9316

0.00

10.00

20.00

30.00

40.00

50.00

60.00

70.00

0 20000000 40000000 60000000 80000000 100000000

Total flow into Alachua Sink (m3)

Surface Elevation (ft)

Figure 7. Correlation between the surface elevation of Alachua Sink and total flow into 

the waterbody 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 50

Table 32. Physical characteristics of Alachua Sink in 2003 and 2004 

Sampling Events Surface Elevation 

(ft) 

Volume 

(m3) 

Surface Area 

(m2) 

Mean Depth 

(m) 

Water 

Residence 

(days) 

30-Jan-03 45.38 33,655 34,741 0.969 - 

5-Feb-03 45.4 33,826 34,873 0.970 - 

12-Feb-03 45.82357 37,554 37,689 0.996 0.390 

12-Mar-03 55.22 171,904 74,290 2.314 0.754 

27-Mar-03 55.7675 182,780 72,941 2.506 0.781 

7-May-03 55.855 184,549 72,670 2.540 0.849 

22-May-03 55.6425 180,267 73,301 2.459 0.822 

9-Jun-03 55.725 181,924 73,067 2.490 0.852 

16-Oct-03 56.59 199,750 69,772 2.863 1.022 

17-Nov-03 55.08 169,177 74,543 2.270 - 

9-Dec-03 52.99 131,073 74,287 1.764 0.756 

31-Dec-03 48.8 69,413 56,891 1.220 - 

7-Jan-04 48.747 68,759 56,576 1.215 - 

11-Feb-04 49.58 79,403 61,329 1.295 0.794 

19-May-04 46.2 41,035 40,202 1.021 1.434 

23-Jun-04 45.376 33,621 34,715 0.968 - 

11-Aug-04 45.112 31,406 32,973 0.952 - 

23-Sep-04 57.72 224,299 62,994 3.561 1.035 

Annual Mean 

(2003) 52.36 131,323 62,422 1.947 0.778 

Annual Mean 

(2004) 48.79 79,754 48,131 1.502 1.088 

Table 33. Bathymetry data for Alachua Sink 

National Geodetic Vertical Datum 

(NGVD) Elevation 

(ft) 

Volume Below 

(ft3) 

Surface Area 

(ft2) 

35 0 0 

36 0 0 

37 1,406 3,762 

38 28,717 36,341 

39 84,125 60,077 

40 166,811 95,556 

41 283,386 126,625 

42 426,919 154,287 

43 598,705 181,714 

44 792,130 206,824 

45 1,009,316 260,284 

46 1,312,134 367,883 

47 1,689,643 486,161 

48 2,111,866 576,256 

49 2,574,655 637,523 

50 3,050,122 681,805 

51 3,527,167 703,873 

52 4,004,651 707,087 
51 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 34. Calculating the volume, surface area, and mean depth of Alachua Sink, 2000–

02 

Year Total Flow 

(m3) 

Calculated 

surface 

elevation 

(ft) 

Calculated sink 

volume 

(m3) 

Calculated 

surface area 

(m2) 

Calculated 

mean depth 

(m) 

2000 17,303,721 42.2 12,155 15,581 0.78 

2001 20,401,573 42.8 15,345 18,768 0.82 

2002 23,672,289 43.4 18,938 22,204 0.85 

Mean 20,459,194 42.8 15,480 18,851 0.82

Table 35. Precipitation and evaporation (m/yr) 

Year Precipitation Evaporation 

2000 0.87 1.66 

2001 1.07 1.48 

2002 1.41 1.48 

Mean 1.12 1.54

SE 0.2 0.1 

2003 1.18 1.65 

2004 1.48 1.48 

Table 36. Measured TN, TP, and Chla concentrations of Alachua Sink 

Year TN 

(mg/L) 

TP 

(mg/L) 

Chla 

(μg/L) 

2000 4.51 1.182 46.3 

2001 4.82 1.353 33.2 

2002 3.65 1.302 43.0 

Mean 4.33 1.279 40.8 

SE 0.35 0.051 3.93 

CV 8% 4% 10% 

2003 2.78 0.63 8.15 

2004 2.07 0.58 13.0 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 52

Table 37. Alachua Sink flow and TN and TP concentrations of different sources, 2000–02 

Land Use Type or Source Flow 

(hm3/yr) 

TN 

(mg/L) 

TP 

(mg/L) 

Forest/rural open 0.74 1.19 0.04 

Urban open 0.75 1.10 0.13 

Agricultural 0.49 2.23 0.34 

Low-density residential 0.60 1.22 0.11 

Medium-density residential 5.49 1.58 0.18 

High-density residential 0.46 1.67 0.29 

Transportation, communications, and utilities 0.21 1.44 0.20 

Rangeland 0.05 1.08 0.04 

Water/wetland 1.37 0.73 0.13 

Main Street WWTP 8.10 4.95 1.19 

J. R. Kelly Generating Station 0.18 2.01 0.90 

Alachua Lake (1)* 1.34 0.16 

* Because no flow data from Alachua Lake to Alachua Sink were available at the control structure between them from 2000 through

2002, the flow from Alachua Lake to Alachua Sink was characterized through Bathtub calibration to fit the predicted TN and TP 

concentrations to the measured TN and TP concentrations of Alachua Sink. 

Table 38. Alachua Sink flow and TN and TP concentrations of different sources in 2003 

Land Use Type or Source Flow 

(hm3/yr) 

TN 

(mg/L) 

TP 

(mg/L) 

Forest/rural open 0.29 1.19 0.04 

Urban open 0.73 1.10 0.13 

Agricultural 0.10 2.23 0.34 

Low-density residential 0.22 1.22 0.11 

Medium-density residential 5.12 1.58 0.18 

High-density residential 0.19 1.67 0.29 

Transportation, communications, and utilities 0.18 1.44 0.20 

Rangeland 0.03 1.08 0.04 

Water/wetland 1.15 0.73 0.13 

Main Street WWTP 9.03 4.58 0.77 

J. R. Kelly Generating Station 0.14 2.02 0.91 

Alachua Lake 63.5 1.94 0.15 

Table 39. Alachua Sink flow and TN and TP concentrations of different sources in 2004 

Land Use Type or Source Flow 

(hm3/yr) 

TN 

(mg/L) 

TP 

(mg/L) 

Forest/rural open 0.36 1.19 0.04 

Urban open 0.92 1.10 0.13 

Agricultural 0.13 2.23 0.34 

Low-density residential 0.27 1.22 0.11 

Medium-density residential 6.41 1.58 0.18 

High-density residential 0.24 1.67 0.29 

Transportation, communications, and utilities 0.24 1.44 0.20 

Rangeland 0.04 1.08 0.04 

Water/wetland 1.41 0.73 0.13 

Main Street WWTP 7.61 3.94 0.52 

J. R. Kelly Generating Station 0.33 2.02 0.91 

Alachua Lake 99.4 1.62 0.15 
53 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

To calibrate the model, each source of TN and TP was designated as an independent tributary. 

Flow and the TN and TP concentrations of the flow were defined for each tributary as listed in 

Tables 37 through 39. The septic tank TN and TP flux into Alachua Sink were calculated as 

previously described, with values of 145.6 milligrams of nitrogen per square meter per day 

(mgN/m2

/day) and 51.8 milligrams of phosphorus per square meter per day (mgP/m2/day) for 

the period from 2000 through 2002, and 76.9 mgN/m2

/day and 26.6 mgP/m2/day for 2003. 

Septic tank inputs of TN and TP were 124.2 mgN/m2

/day and 42.9 mgP/m2/day for 2004. 

As discussed in the previous section for Alachua Lake modeling, the settling velocity submodel 

was chosen to estimate the in-lake concentrations of TN and TP. 

Calibration factors were applied to fit TN and TP predictions to the measured data. Bathtub 

provides two calibration methods for phosphorus and nitrogen: Method 0 calibrates decay 

rates, and Method 1 calibrates concentration. In the first case, the calibration factors are 

applied to estimated sedimentation rates in computing nutrient balances. In the second case, 

the factors are applied to estimated concentrations. In Method 0, it is assumed that the error is 

attributed primarily to the sedimentation model. In Method 1, the error source is unspecified 

(some combination of input error and sedimentation model error). The latter may be used when 

predicted nutrient profiles are insensitive to errors in predicted sedimentation rate, because the 

mass balance is dominated by inflow and outflow terms (low hydraulic residence times) (Walker, 

1999). In this study, Method 1 was adopted to calibrate the concentration in Alachua Sink. 

Typical calibration factors for TN and TP recommended by the Bathtub User’s Manual are 0.5 to 

2.0 for TP and 0.33 to 3 for TN. In this analysis, 2.0 and 1.3 were used for calibrating TP and 

TN for all the simulations. Method 0 was adopted to calibrate decay rates for Alachua Lake 

based on its greater residence time and limited water quality data. Calibration factors of 0.9 and 

1.5 were used for calibrating TP and TN for all simulations. Table 40 shows the results of the 

model calibration. 

Table 40. Bathtub calibration results for Alachua Sink 

TN (mg/L) TP (mg/L) 

Measured Predicted Error Measured Predicted Error

2000 4.51 4.04 -10.4% 1.18 0.77 -35.1% 

2001 4.82 4.33 -10.1% 1.35 1.19 -11.9% 

2002 3.65 3.44 -5.7% 1.30 1.10 -15.1% 

Composite 

2000–02 4.33 3.95 -8.8% 1.28 1.05 -17.7% 

2003 2.78 2.85 2.5% 0.63 0.46 -26.9% 

2004 2.07 2.30 11.1% 0.58 0.37 -36.2% 

As noted previously, flow from Alachua Lake to Alachua Sink from 2000 through 2002 was 

estimated during the Bathtub calibration. The calibrated flow during this period was 1 hm3

/year 

(about 810 acre-feet/year). Simulation results for nitrogen were close to observed values, while 

phosphorus was consistently underpredicted. Part of this underprediction is likely due to the 

limited total phosphorus data available for the Main Street WWTF. Typically only 3 to 4 total 

phosphorus values were available in a given year (2000 has only 1 total phosphorus value), and 

averages for individual years ranged from 0.53 mg/L (2000 and 2004) to 1.07 mg/L (2002). 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 54

y = 7E-09x + 0.3455

R2 = 0.6108

0.000

0.200

0.400

0.600

0.800

1.000

1.200

0 20000000 40000000 60000000 80000000 100000000

TOTAL FLOW INTO ALACHUA SINK (m3)

WATER RESIDENCE TIME (DAYS)

Figure 8. Correlation between water residence time τo and total flow into Alachua Sink 

The Bathtub model could not be used to estimate chla concentrations for Alachua Sink, 

because all of the eutrophication response submodel options provided with Bathtub assume a 

steady-state condition where the water residence time is long enough for the phytoplankton 

biomass to respond to changes in TN and TP concentrations. This assumption in the model 

allows the use of characteristic regression curves to predict chla concentrations from TN and TP 

concentrations. The volume of Alachua Sink was only about 12.6 acre-feet (15,480 m3

) from 

2000 through 2002, and 94.3 acre-feet (116,355 m3

) in 2003. The average annual flow from all 

the point and nonpoint sources into Alachua Sink was 15,922 acre-feet (19,648,200 m3

) from 

2000 through 2002, 65,438 acre-feet (80,750,000 m3

) for 2003, and 95,105 

acre-feet (117,360,200 m3

) for 2004. Given the above volumes and flows, and assuming a 

completely mixed waterbody where evaporation balances precipitation, the water residence time 

for Alachua Sink was about 1.13 days from 2000 through 2002, 0.78 days for 2003, and 1.09 

days for 2004. This residence time is not sufficient to allow the phytoplankton to fully use all the 

available nutrients in the water (most empirical relationships between chla and nutrient 

concentrations were developed based on ANNUAL chla concentrations and ANNUAL nutrient 

concentrations). Therefore, this analysis did not use an empirical model. Instead, chla

concentrations in Alachua Sink were estimated using the following equation: 

 

AQVAKAQV dt

da

inin += − out ***** (5) 

 

where: 

 da/dt is the change rate of chla in Alachua Sink, 

 V is the volume of Alachua Sink, 

 Qin is the inlet flow, 
55 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

 Ain is the inlet chla concentration, 

K is the intrinsic growth rate of phytoplankton, which is usually considered about 0.5/day 

under natural conditions (Chapra, 1997), 

 A is the chla concentration of Alachua Sink, and 

 Qout is the outlet flow. 

Assuming that Alachua Sink is at a steady state: 

= 0

dt

da (6) 

Therefore: 

inin += − out  0 AQVAKAQ (7) 

Re-arranging Equation (7), 

out − = ** )*( AQAVKQ inin (8) 

and 

 

)*(

*

VKQ

AQ A out

inin

− = (9) 

Assuming Qin = Qout (i.e., the volume of Alachua Sink did not change during the period of 

analysis) Equation (9) can be converted to: 

K τ )*1(

A A in

− = (10) 

Where: 

τ is the water residence time of Alachua Sink (Alachua Sink). 

In this analysis, Ain was calculated as the mean chla concentration of Sweetwater Branch and 

Alachua Lake weighted over the flow from these two sources. Table 41 lists the mean value of 

the measured chla concentration for Sweetwater Branch, based on data provided by the 

SJRWMD (2000 through 2002), GRU and JEA (2003 and 2004), and the ACEPD (2003 and 

2004). The mean flow of Sweetwater Branch was predicted from the WWM model for each 

year, while the Bathtub model was used to predict the mean flow from Alachua Lake in 2003 

and 2004. A mean flow of 1 hm3

 (1x106 m3) was used for the discharge from Alachua Lake from 

2000 through 2002. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 56

Table 41. Annual average flow and chla concentrations in Sweetwater Branch and 

Alachua Lake used to calculate Ain

Parameter Sweetwater 

Branch 

Alachua 

Lake 

Flow (acre-feet) (2000–02) 15,112* 810** 

Flow (acre-feet) (2003) 13,922* 51,459 

Flow (acre-feet) (2004) 14,554* 80,551 

Average annual chla (μg/L) (2000–02) 0.51 6.51*** 

Average annual chla (μg/L) (2003) 2.02 6.51*** 

Average annual chla (μg/L) (2004) 1.60 9.28 

Ain (μg/L) (2000–02) 0.80 

Ain (μg/L) (2003) 5.55 

Ain (μg/L) (2004) 8.10 

* The flow from Sweetwater Branch includes the discharges from the Main Street WWTP and John 

R. Kelly Generating Station and the surface runoff created in the Upper Sweetwater Branch, Lower 

Sweetwater Branch, and Extension Ditch sub-basins. 

** Measured data were not available. This value was characterized in the Bathtub calibration for 

Alachua Sink for the period from 2000 through 2002. 

*** Because of the thick mat of floating aquatic plants in the channels from Alachua Lake to 

Alachua Sink, chla concentration in the flow from Alachua Lake to Alachua Sink could not be 

modeled. This value is the mean chla concentration of the measured chla concentration of the 

May 22 and June 9 sampling trips in 2003. During these two trips, Alachua Lake was considered 

to be at its steady state. 

The water residence time for Alachua Sink was calculated by dividing the volume of Alachua 

Sink by the total flow into Alachua Sink, assuming the waterbody was completely mixed. 

However, the inlet from Alachua Lake to Alachua Sink and the outlet from Alachua Sink to the 

primary sink feature are so close to each other that the complete mixing of Alachua Sink by the 

inlet water from Alachua Lake may not happen regularly. This was in fact demonstrated by a 

study of the spatial distribution of the chla concentration across Alachua Sink conducted by JEA 

(2003); the study showed that the chla concentration at the sampling site farthest away from the 

inlet could be higher than the chla concentration right at the inlet. This indicates that the τ, 

which is the actual water residence time of phytoplankton communities in Alachua Sink, could 

be longer than what is predicted by only considering the volume of Alachua Sink and total flow 

into Alachua Sink (τ0) because of the existence of the nonmixed area. 

Because the actual τ of the phytoplankton community could not be calculated by simply dividing 

the volume of Alachua Sink by the total flow, a ratio was calculated between the actual τ of 

phytoplankton and the water residence time calculated by dividing the volume of Alachua Sink 

by the total flow into Alachua Sink (τ0). This ratio was later used to calculate the τ after the 

hydrology of the watershed was changed due to a change in the land use pattern and/or the 

removal of point sources. 

To determine the actual τ, the measured in-lake chla concentration (A) and the average chla

concentration in the inlet water (Ain) (Table 39) were substituted into Equation (10) to solve for τ. 

By assuming that the phytoplankton intrinsic growth rate is 0.5/ days, the estimated τ is about 

1.96 days, based on an annual average chla concentration of 40.8 μg/L for Alachua Sink from 

2000 through 2002 (Table 36). This yields a ratio between τ and τ0 (1.13 days as calculated 

previously) of 1.73 for the period from 2000 through 2002. For 2003, the τ calculated using the 

same method is 0.64 days based on an annual mean chla concentration of 8.15 μg/L (Table 36)

and an average Ain of 5.55 μg/L (Table 41). The τ0 calculated previously was 0.69. The τ/τ0
57 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

ratio for 2003 was 0.94. In 2004, the τ calculated was 1.46 days, based on an annual mean 

chla concentration of 29.77 μg/l and an average Ain of 8.10 μg/l. The τ/τ0 ratio for 2004 was 

1.33. Except for 2003, the calculated τ/τ0 ratio exceeded 1, indicating that the exposure time of 

phytoplankton to nutrients and the time available for growth were greater than the simple 

hydraulic residence time calculated by the Bathtub model. According to Jim Weimer (personal 

communication), Paynes Prairie Park biologist, 2003 was the first time that he had seen 

Alachua Sink completely covered by floating macrophytes (this was the case by October 2003). 

Consequently, although nutrients were readily available in 2003, floating macrophytes limited 

the available light for phytoplankton growth in the water column, and increased plant biomass 

was in the form of macrophytes rather than algal chlorophyll. 

5.3.2 Determination of Wet and Dry Periods for Model Simulation and TMDL 

Development 

Annual rainfall records for Gainesville from 1897 through 1995 were obtained from Rao et al. 

(1997) and updated through 2004. Over this period of record, the annual rainfall average was 

51.3 inches. Figure 8 illustrates the long-term rainfall pattern along with cumulative frequency 

information. For example, the 25th percentile for annual rainfall is 46.63 inches, meaning that 

75% of the years have rainfall totals that exceed 46.63 inches. The years 2000, 2001, and 2003 

were in the 16th–25th percentile, while 2002 and 2004 were in the 70th–78th percentile with 

respect to annual rainfall. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 58

GAINESVILLE ANNUAL RAINFALL

20

25

30

35

40

45

50

55

60

65

70

75

80

18971905191319211929193719451953196119691977198519932001

YEAR

RAINFALL (INCHES)

HISTORICAL RAIN STATISTICS 

Rainfall 

(inches) 

N of cases 108 

Minimum 32.79 

Maximum 76.95 

Median 50.415 

Mean 51.298 

95% CI Upper 52.917 

95% CI Lower 49.679 

Standard Dev 8.488 

1% 33.24 

5% 36.73 60% 52.78

10% 40.79 70% 55.33

20% 45.56 75% 56.83

25% 46.63 80% 59.66

30% 47.31 90% 62.21

40% 48.93 95% 64.13

50% 50.42 99% 74.83

Figure 9. Annual rainfall at Gainesville, 1897–2004 
59 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

It was noted earlier that annual rainfall totals were below average for 1999 through 2001. The 

frequency of cycles of wet or dry periods was explored by calculating a running 3-year average 

annual rainfall total over the period of record (Figure 10). The 1999–2001 average of 44.56 

inches represented the 11th percentile. The 2001–03 average of 48.03 inches ranked at about 

the 25th percentile. When the 2002–04 period was ranked, the average of 53.43 inches was at 

the 68th percentile. It appears that the 2000–04 period encompassed some rather large ranges 

in individual yearly rain totals, as well as large ranges in multiple-year averages, such as the 3-

year average presented here. 

GAINESVILLE 3 YEAR RAINFALL AVERAGE

30

40

50

60

70

18971905191319211929193719451953196119691977198519932001

STARTING YEAR

3 YEAR AVERAGE (INCHES)

Figure 10. Running three-year average rainfall for Gainesville 

Flow records for the Sweetwater Branch gauging site near Williston Road were also evaluated 

with respect to the influence of the Main Street WWTP flow. Figure 11a illustrates daily flow 

records at this site from 1998 through 2004. Daily flows for Sweetwater Branch are plotted 

along with the daily discharge flows from the Main Street WWTF (Brett Goodman, GRU, 

personal communication). Cumulative frequency plots are provided for daily flow at the site with 

and without the Main Street WWTP contribution (Figure 11b). Table 44 summarizes various 

flow percentiles based on the total flow at the Sweetwater gauge, as well as flow with the Main 

Street WWTF flow removed. According to the table, without the Main Street WWTF discharge, 

the 25th percentile is less than 1 cfs, and the 25th percentile flow with the Main Street WWTF is 

nearly 14 times higher. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 60

Figure 11a. Daily flow (cfs) on Sweetwater Branch near Williston Road, 1998–2004 

SWEETWATER BRANCH AT 

WILLISTON ROAD

0

50

100

150

200

250

01/01/9805/01/9809/01/9801/01/9905/01/9909/01/9901/01/0005/01/0009/01/0001/01/0105/01/0109/01/0101/01/0205/01/0209/01/0201/01/0305/01/0309/01/0301/01/0405/01/0409/01/04

DATE

DISCHARGE 

(CFS)

sweetwater mainstreet

Figure 11b. Cumulative frequency flow plot for Sweetwater Branch with and without the 

Main Street WWTP 

0 6

121824303642485460667278849096

102108114120

SWEETWATER FLOW WITH MAINSTREE

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

F

R

A

C

TIO

N

O

F

D

A

T

A

-10 -4 2 8

142026323844505662687480869298

104110

SWEETWATER FLOW WITHOUT MAINSTREET

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

F

R

A

C

T

OI N

O

F

D

A

T

A
61 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 42. Percentile flow at the Sweetwater Branch gauge with and without the Main 

Street WWTF, 1998–2004 

Percentile 

With Main 

Street 

(cfs) 

Without Main 

Street 

(cfs) 

5 7.24 -1.18 

10 8.13 -0.25 

25 8.96 0.65 

50 10.84 1.63 

75 13.52 3.73 

90 17.41 7.65 

95 23.00 11.67 

99 47.00 33.27 

Based on the historical record, a dry-weather critical condition corresponding to the 25th

percentile of rainfall (46.6 inches) and a wet-weather critical condition corresponding to the 75th

percentile of rainfall (56.7 inches) were selected for simulation and use in TMDL development. 

From 2000 through 2004, there were individual years that bracketed each of these percentiles, 

and the model calibration of these individual years presented earlier supported the continued 

application of the models to establish nutrient TMDLs for Alachua Sink. 

5.3.3 Evaluating the Background TSI of Alachua Sink 

Two scenarios were analyzed for the background TSI of Alachua Sink. For the first scenario, 

the discharges from the two point sources (the Main Street WWTP and John R. Kelly 

Generating Station) were kept, but the TN and TP concentrations from these facilities were 

reduced to the EMC level of forest/rural open land. For the second scenario, the discharges 

from the two facilities were totally removed. 

In addition to the above modification of the TN and TP loadings, the following procedures were 

followed to analyze the background TSI of Alachua Sink for both scenarios: 

• All the man-made land use categories (urban open; agricultural, low-, medium-, and 

high-density residential; transportation and communication; and rangeland) in both the 

watershed areas that discharge into Sweetwater Branch, directly to Alachua Sink, and 

into Alachua Lake were evaluated as forest/rural open. All of the loadings from septic 

tanks were also removed. 

• TN and TP loadings through surface runoff into both Sweetwater Branch, directly to 

Alachua Sink, and Alachua Lake were then re-estimated for both a dry year and a wet 

year using the calibrated WMM. 

• TN and TP concentrations from forest/rural open and water/wetland were calculated by 

dividing the total loadings by the total flow from the watershed. 

• TN and TP concentrations of the flow from Alachua Lake to Alachua Sink were reestimated using the Bathtub model set up previously for Alachua Lake. TN and TP 

concentrations for Prairie Creek were reduced to 1.192 mg/L and 0.068 mg/L, 

respectively. These are the concentrations for Newnans Lake, assuming the attainment 

of the nutrient TMDL for Alachua Sink (Gao and Gilbert, 2003). Based on TN data 

provided by Carol Lippincott (personal communication) of the SJRWMD that 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 62

documented a consistent reduction in TN between 2 monitoring locations in Prairie 

Creek, the TN concentration was further reduced to 0.88 mg/L. 

The dry-weather critical condition simulated (46.6 inches of rainfall) was very similar to the 

climatic and hydrologic conditions present in 2003. The Bathtub model was used to simulate 

the natural background dry-weather conditions for Alachua Lake. Based on the simulation, the 

annual flow from Alachua Lake to Alachua Sink was 52.0 hm3

. The Main Street WWTP and 

John R. Kelly Generating Station plant flows were set at 9.03 hm3

 and 0.14 hm3, respectively. 

The wet-weather critical condition rainfall was slightly less than the total recorded in 2004. 

Again a Bathtub model simulation was completed to determine the flow and nutrient 

contributions from Alachua Lake. Under the wet-weather critical condition, the annual discharge 

from Alachua Lake was 74.6 hm3

. The Main Street WWTP and John R. Kelly Generating 

Station plant flows were set at 9.03 hm3

 and 0.18 hm3, respectively. 

Table 43. Background flow and TN and TP concentrations of surface runoff into Alachua 

Sink and Alachua Lake in a dry year 

Land Use Type or Source 

Flow to Alachua 

Sink 

(hm3/yr) 

Flow to Alachua 

Lake 

(hm3/yr) 

TN concentration 

(mg/L) 

TP concentration 

(mg/L) 

Forest/rural open 1.75 9.73 1.190 0.040 

Water/wetland 1.13 25.68 0.730 0.130 

Main Street WWTP 9.03 - 1.190 0.040 

J. R. Kelly Generating Station 0.14 - 1.190 0.040 

Alachua Lake Bathtub predicted - Bathtub predicted Bathtub predicted 

Prairie Creek - 30 0.88 0.068 

- 

Table 44. Background flow and TN and TP concentrations of surface runoff into Alachua 

Sink and Alachua Lake in a wet year 

Land Use Type or Source 

Flow to Alachua 

Sink 

(hm3/yr) 

Flow to Alachua 

Lake 

(hm3/yr) 

TN concentration 

(mg/L) 

TP concentration 

(mg/L) 

Forest/rural open 2.13 11.83 1.190 0.040 

Water/wetland 1.37 31.23 0.730 0.130 

Main Street WWTP 9.03 - 1.190 0.040 

J. R. Kelly Generating Station 0.18 - 1.190 0.040 

Alachua Lake Bathtub Predicted - Bathtub predicted Bathtub predicted 

Prairie Creek - 40 0.88 0.068 

The flow and TN and TP concentrations of surface runoff from forest/rural open, water/wetland, 

and Alachua Lake into Alachua Sink were then entered into the calibrated Bathtub model to reestimate the in-lake TN and TP concentrations. As presented in Table 41, a mass balance 

approach was used to estimate an average chla concentration (Ain) that entered Alachua Sink 

based on flow rates and chla concentrations from Sweetwater Branch and Alachua Lake. 

Following a similar approach for the critical background wet and dry scenarios, chla

concentrations of 8.64 μg/l and 8.16 μg/l were calculated for the dry natural conditions with and 

without point sources at forest concentrations. Chla concentrations of 8.16 μg/l and 8.91 μg/l 
63 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

were calculated for the wet natural conditions with and without point sources at forest 

conditions. 

Water residence times in 2003 and 2004 averaged 0.78 days and 1.09 days, respectively. 

Comparisons between the algal biomass levels in Alachua Sink from 2000 through 2004 and 

inflow concentrations indicated that phytoplankton residence times exceeded the water 

residence times by up to a factor of 2. Water residence times calculated by the Bathtub model 

for the background wet and dry scenarios were multiplied by a factor of 1.5 to yield residence 

times of 1.20 days for the dry scenario and 0.71 days for the wet scenario. Based on Equation 

(10), the corresponding chla concentrations in Alachua Sink for the natural background dry and 

wet conditions with point sources at forest conditions would be 20.1 μg/l and 11.7 μg/l, 

respectively. Chla concentrations in Alachua Sink for the background dry and wet conditions 

without the point sources would be 20.3 μg/l and 13.8 μg/l, respectively. 

The TSI represents the average of a TSINUT and a TSICHL. The Bathtub model provided 

acceptable predictions for annual TN and TP concentrations in Alachua Sink over a variety of 

hydrologic conditions for the 2000–04 period. Chlorophyll predictions were problematic for a 

variety of reasons, however, including the response of the Alachua Lake and Alachua Sink 

systems to increased rainfall after a prolonged dry period, as well as the proliferation of floating 

macrophytes in both systems. Portions of Sweetwater Branch are periodically covered by 

floating macrophytes as well as emergent macrophytes; these compete with phytoplankton for 

nutrients and limit available light for phytoplankton growth. Alachua Lake/Paynes Prairie is an 

extensive wetland system where emergent and floating macrophytes dominate over 

phytoplankton. In addition, the Alachua Sink waterbody represents a rather small, shallow 

system, particularly with respect to the application of lake or reservoir models to predict steadystate chla levels. Finally, as seen in the available data, chla concentrations could change 

dramatically (spatially and temporally) and even the existing information was not likely to fully 

capture and characterize those fluctuations. 

Consequently, the TMDL focused on the TSINUT component of the TSI. It should also be noted 

that there is a growing concern statewide regarding the quality of surface water that enters the 

aquifer system via both natural and man-made pathways. The state continues to fund a number 

of research and remediation projects to reduce nitrogen, particularly nitrates in ground water 

and springs. The background TSINUT, with point source discharges set at forest EMC 

concentrations, was 68.04 for the dry period and 65.86 for the wet period. The natural 

background TSI with no point source discharges was 67.87 for the dry period and 65.46 for the 

wet period. Based on current Department practice, where the natural background TSI of a lake 

is different from the target TSI in Rule 62-303, F.A.C., natural background plus 5 TSI units will 

be used as the target for TMDL development. In this case, the TN and TP loadings under the 

TMDL should be those loads that result in a TSI of no more than 73.04 in dry periods and 70.86 

in wet periods. 

Table 45. Simulated natural background TN and TP concentrations for Alachua Lake in 

dry and wet years 

Variable Dry year Wet year

TP (mg/L) 0.089 0.080 

TN (mg/L) 1.14 1.01 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 64

Table 46. Simulated background TN, TP, and chla concentrations and TSI for Alachua 

Sink in dry and wet years 

Variable 

Dry Year Wet Year

Point Source 

Discharge 

Not Removed 

Point Source 

Discharge 

Removed 

Point Source 

Discharge 

Not Removed 

Point Source 

Discharge 

Removed 

TP (mg/L) 0.162 0.176 0.152 0.160 

TN (mg/L) 1.481 1.469 1.338 1.313 

Chla (μg/L) 20.5 20.1 11.7 13.8 

TSINUT 68.04 67.87 65.86 65.46 

5.3.4 Summary of TN and TP Loading for Current and Background Conditions 

Table 47 summarizes the TN and TP loadings into Alachua Sink from point and nonpoint 

sources under current conditions and background conditions. Based on Table 46, the natural 

background TSINUT for Alachua Sink is between 65.48 and 68.04, depending on the climatic 

condition and whether a background point source flow is included. 

Critical Condition 

Table 48 lists the current and background TN and TP loadings from major sources to Alachua 

Sink during the period of this analysis. For the current condition, the TN and TP loadings are 

382,062 lbs/yr and 40,478 lbs/yr for the dry year, and 462,457 lbs/yr and 91,888 lbs/yr for the 

wet year, respectively. Because the goal of TMDL development is for a waterbody segment to 

meet water quality criteria all the time, whether it is a dry-weather condition or a wet-weather 

condition, the TMDL for Alachua Sink was based on 2 separate conditions. A dry-year loading 

was used as the critical condition for the NPDES facilities that discharge to Alachua Sink 

(TSINUT limit of 73.04), and a wet-year loading was used as the critical condition for the NPDES 

municipal separate storm sewer system (MS4) and load allocation (LA) portion of the TMDL 

(TSINUT limit of 70.86). 

The model was then used to estimate the TN and TP loadings that result in a TSINUT of 73.04. 

To reduce the TN and TP loadings during the dry year, some portions of the area of human land 

use categories were changed to have the runoff coefficients and EMCs of the forest/rural open 

land area. At the same time, the same percent load reduction was applied to the point sources 

by allowing the current TN and TP concentrations (Main Street WWTF discharge assumed TN 

and TP concentrations of TN = 4.46 mg/L, TP = 0.77 mg/L) of the discharges to remain the 

same, but the discharge flow from the Main Street WWTF was gradually reduced. No changes 

were made to the John R. Kelly Generating Station discharge. Using the above calibrated 

models, a 54.5% reduction in TN loading from the current dry condition is required to achieve 

the target, and the allowable TN loading is 40,380 lbs/yr. This corresponds to a daily discharge 

of 2.97 mgd at a total nitrogen concentration of 4.46 mg/L from the Main Street WWTP. Table 

48 lists the detailed TN and TP loadings from different sources. 

Because the wet-year natural background TSINUT is 65.86, the appropriate TSINUT threshold for 

wet years is 70.86. A similar procedure was followed to determine the level of reduction from 

the current wet-weather loading level necessary to achieve the target. Based on the calibrated 

models above, wet-weather loadings need to be reduced by 44.4% to reach the target (Figure 

13). Table 48 lists the TN and TP loadings from the different sources. 
65 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 47. Alachua Sink TN and TP loadings (lbs/yr) from point and nonpoint sources under current and 

conditions 

Sources 

Current Condition Background Condition 

Dry Year Wet Year 

Dry Year W

Point Source 

Discharge Not 

Removed 

Point Source 

Discharge 

Removed 

Point Source 

Discharge Not 

Removed 

TP TN TP TN TP TN TP TN TP TN 

Watershed 2,928 24,642 3,551 29,910 497 6,984 497 6,984 581 7,800 

Septic Tanks 1,326 3,837 1,614 4,667 0 0 0 0 0 0 

Precipitation 8 16 11 23 8 16 8 16 11 23 

Main Street 

WWTP 15,329 88,748 15,329 88,748 796 23,690 0 0 796 23,69

J. R. Kelly 

Generating 

Station 

281 623 361 802 12 367 0 0 16 472 

Alachua Lake 20,606 264,196 71,022 338,307 10,203 130,230 10,203 130,230 13,157 166,10

Total 40,478 382,062 91,888 462,457 11,516 161,287 10,708 137,230 14,561 198,09
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 66

y = -7.0617x + 570.29

R2

 = 0.9199

0

10

20

30

40

50

60

70

80

90

100

40 50 60 70 80 90

TSI (NUT)

% REDUCTIO

N

Figure 12. Correlation plot of TSINUT versus reduction from the current dry-condition 

case 

y = -11.528x + 861.29

R2

 = 0.9925

0

10

20

30

40

50

60

70

80

90

100

55 60 65 70 75 80 85

TSI (NUT)

% REDUCTIO

N

Figure 13. Correlation plot of TSINUT versus reduction from the current wet-condition 

case 
67 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 48. TN and TP loadings from different sources resulting in the target TSI (lbs/yr) 

Dry Year Wet Year 

TP TN TP TN 

Watershed 1,586 14,255 2,245 20,111 

Precipitation 8 16 11 23 

Main Street WWTP 6,975 40,380 6,975 40,380 

J. R. Kelly Generating 

Station 281 623 361 801 

Alachua Lake 12,954 149,596 17,565 195,007 

Total 21,804 204,870 27,157 256,322

Load reduction (lbs/yr) 18,674 177,192 64,731 206,135

Percent load reduction 

(lbs/yr) 46% 46% 70% 45% 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 68

Chapter 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 [WLAs]), nonpoint source loads (load allocations 

[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 TMDL equation may not sum up to the 

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

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

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 best management 

practices (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. The nutrient TMDL for Alachua Sink (Table 49) is expressed in terms of 

lbs/yr and/or percent reduction. Based on a TN/TP ratio smaller than 10 for the current 

condition, TN is the limiting nutrient for Alachua Sink phytoplankton communities and the 

Alachua Sink TMDL was only developed for TN loadings (Table 49).
69 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Table 49. TMDL Components 

WBID Parameter 

WLA 

LA 

(lbs/yr)2 MOS TMDL (lbs/yr)2 Percent Reduction Wastewater 2

(lbs/yr)1 NPDES Stormwater2

2720A TN 41,003 45% reduction 215,319 Implicit 256,322 45% 

1

 Based on the critical dry-period (dry) allowable loadings. 2

 Based on the wet-period allowable loadings and contains the total allowable stormwater loading (NPDES stormwater and nonNPDES stormwater). 

Note: The low-flow loadings represent the water quality–based effluent limit (WQBEL) for the facilities. As this loading is based on 

dry-weather conditions with a limited nonpoint source contribution, pollutant trading with nonpoint sources would not be appropriate 

at this time. 

It should be noted that, for this TMDL, the Department did not follow the “standard” three-step 

allocation procedure outlined in the Report to the Governor and the Legislature on the Allocation 

of Total Maximum Daily Loads in Florida (Department, February 1, 2001). However, as 

described in the report, the Department should use its best professional judgment to determine 

whether all of the allocation steps are warranted in a given TMDL. For this TMDL, the 

Department allocated loadings between point and nonpoint sources based on dry- and wet-year 

conditions, respectively, rather than sequentially reducing nonpoint sources and then point 

sources. This approach was appropriate because the point sources are the dominant source of 

TN loading during dry-weather conditions, particularly during very low-flow conditions under 

which WQBELs for point sources are typically determined. 

6.2 Load Allocation 

The total allowable nonpoint loading is 215,319 lbs/yr for TN. Given that current TN nonpoint 

source loadings were 372,907 lbs/yr for the wet year, the TMDL requires a 45% reduction in 

existing nonpoint source loadings to the Alachua Sink watershed. This represents the 

combined nonpoint loading from MS4 areas, as well as discharges regulated by the Department 

and the water management districts that are not part of the NPDES Stormwater Program (see 

Appendix A). 

It should be noted that the TMDL developed for Alachua Sink assumes that the Newnans Lake 

TMDL will be met. Nitrogen and phosphorus TMDLs were adopted for Newnans Lake and limit 

the annual load of TN and TP to the lake to 85,470 lbs and 10,924 lbs, respectively. 

6.3 Wasteload Allocation 

6.3.1 NPDES Wastewater Discharges 

The WLAs for NPDES wastewater discharges are 40,380 lbs/yr of TN for the Main Street 

WWTP (FL0027251) and 623 lbs/yr of TN for the John R. Kelly Generating Station 

(FL0026646). The WLA was based on the water quality data measured from 2000 through 

2004. Both a critical dry and wet condition were simulated to assess the impacts associated 

with point and nonpoint source discharges to Alachua Sink. In both cases, a 54.5 % reduction 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 70

of the point source loading from current conditions was needed to achieve the corresponding 

TSINUT targets. 

TN loading from point sources, especially the loading from the Main Street WWTP, played a 

very important role in influencing the water quality of Alachua Sink. Of the existing dry-year total 

of 382,062 lbs of TN discharged into Alachua Sink (Table 44), the Main Street WWTP currently 

contributes 88,748 lbs, which represents about 23% of the total current critical period TN 

loading into Alachua Sink. The total allowable critical period TN loading is 204,870 lbs/yr of TN. 

6.3.2 NPDES Stormwater Discharges 

As noted in Sections 4 and 6.1, the load from stormwater discharges permitted under the 

NPDES Stormwater Program is placed in the WLA, rather than the LA. This includes loads from 

MS4s. Based on the 2000 census, the Alachua Sink watershed includes areas that are covered 

by the MS4 Program, and the WLA for stormwater discharges is a 45% reduction in current 

loading from the MS4. This percent reduction is the same percent reduction required under the 

LA for nonpoint sources. However, 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 Margin of Safety 

The methodology used to determine this TMDL includes an implicit MOS because it relies on 

the dry-year background TSI as the target for the TMDL. Additional implicit MOSs exist due to 

some of the assumptions made during the modeling process, including the use of maximum 

septic tank loading rates and maximum rates of septic tank failure. 
71 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Chapter 7: NEXT STEPS: IMPLEMENTATION PLAN 

DEVELOPMENT AND BEYOND 

7.1 Basin Management Action Plan 

Following the adoption of this TMDL by rule, the next step in the TMDL process is to develop an 

implementation plan for the TMDL, referred to as the Basin Management Action Plan (BMAP). 

This document will be developed over the next year in cooperation with local stakeholders, who 

will attempt to reach consensus on detailed allocations and on how load reductions will be 

accomplished. The BMAP will include, among other things: 

• Appropriate load reduction allocations among the affected parties, 

• A description of the load reduction activities to be undertaken, including structural 

projects, nonstructural BMPs, and public education and outreach, 

• A description of further research, data collection, or source identification needed in order 

to achieve the TMDL, 

• Timetables for implementation, 

• Confirmed and potential funding mechanisms, 

• Any applicable signed agreement(s), 

• Local ordinances defining actions to be taken or prohibited, 

• Any applicable local water quality standards, permits, or load limitation agreements, 

• Milestones for implementation and water quality improvement, and 

• Implementation tracking, water quality monitoring, and follow-up measures. 

An assessment of progress toward the BMAP milestones will be conducted every five years, 

and revisions to the plan will be made as appropriate, in cooperation with basin stakeholders. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 72

REFERENCES 

ACLD. 2003. Alachua Sink. Alachua County Library District Heritage Collection. 

Brenner, M., and T. J. Whitmore. 1998. Historical sediment and nutrient accumulation rates 

and past water quality in Newnans Lake. Final Report for the St. Johns River Water 

Management District. 

Brown, M. T. 1995. South Dade watershed project. University of Miami and the Southwest 

Florida Water Management District. 

Canfield, D. E., Jr. 1981. Chemical and trophic state characteristics of lakes in relation to 

regional geology. Final report submitted to the Cooperative Fish and Wildlife Research Unit, 

University of Florida. 

Carlson, R. E. 1977. A trophic state index for lakes. Limnology & Oceanography: 22:361-369. 

CDM. 1990. Point and nonpoint source loading assessment, Phase I. Report to the Sarasota 

Bay National Estuary Program. 

Chapra. 1997. Surface Water-Quality Modeling. WCB/McGraw-Hill publishers. 844 pages. 

Clark, W., R. Musgrove, C. Menke, and J. Cagle. 1964. Interim report on the water resources 

of Alachua, Bradford, Clay, and Union Counties, Florida. Florida Geological Information Circular 

# 35. Tallahassee, Florida: State Board of Conservation, Division of Geology. 

Copeland, R., T. Gardner, J. Craft, W. Schmidt, C. M. Browner, H. L. Rhodes, and C. C. Aller. 

1991. Florida’s Ground Water Quality Monitoring Program hydrogeological framework. Florida 

Department of Environmental Regulation. 

Florida Department of Environmental Protection. 2001. Ocklawaha River Group 1 basin status 

report. Tallahassee, Florida: Division of Water Resource Management. 

———. February 1, 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, 

Division of Water Resource Management. 

Gao and Gilbert. 2003. Nutrient Total Maximum Daily Load for Newnans Lake, Alachua 

County, Florida. 78 pages. 

Gido, K. B. 2002. Interspecific comparisons and potential importance of nutrient excretion by 

benthic fishes in a large reservoir. Transactions of the American Fisheries Society 131: 260–

270. 

Gottgens, J. F., and C. L. Montague. 1988. Orange, Lochloosa and Newnans Lakes, a survey 

and preliminary interpretation of environmental research data. Special Publication SJ 87-SP3. 

Gainesville, Florida: Department of Environmental Engineering Sciences, A. P. Black Hall, 

University of Florida. 
73 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Hand, J., J. Col, J., and L. Lord. 1996. Northwest Florida District water quality 1996 305(b) 

technical appendix. Tallahassee, Florida: Florida Department of Environmental Protection. 

Harper, H. H. 1992. Estimation of stormwater loading rate parameters for central and south 

Florida. Orlando, Florida: Environmental Research & Design. 

———. 1994. Stormwater loading rate parameters for central and south Florida. Orlando, 

Florida: Environmental Research & Design, Inc. 

Harper, H. H., and E. H. Livingston. 1999. Everything you always wanted to know about 

stormwater management practices but were afraid to ask. Biennial Stormwater Research 

Conference, Tampa, Florida. 

Holly, J. B. 1976. Stratigraphy and sedimentary history of Newnans Lake. M. S. thesis, 

University of Florida. 

James, R. T., and V. J. Bierman, Jr. 1995. A preliminary modeling analysis of water quality in 

Lake Okeechobee, Florida: Calibration results. Water Research 29: 2755–2766. 

Jones, Edmunds & Associates, Inc. 2003. Personal Communication. 

Jones, Edmunds & Associates, Inc. August 2005. Gainesville Regional Utilities Alachua Sink 

intensive water quality and nutrient loading study, Phase 2. 

Lasi, M. A. 1999. An external nutrient budget for Orange Lake effect of sinkhole seepage on inlake nitrogen and phosphorus stores. Palatka, Florida: St. Johns River Water Management 

District. 

Linsley, R. U., and J. B. Franzini. 1979. Water resources engineering. McGraw-Hill Book Co. 

Nordlie, F. G. 1976. Plankton communities of three central Florida lakes. Hydrobiologia 48 (1): 

65-78. 

Rao, D. V., S. Abe Jenab, and D. Clapp. 1997. Rainfall analyses for northeast Florida: 

Summary of monthly and annual rainfall data through 1995. Special publication SJ97-SP22. 

St. Johns River Water Management District. 

Robison, C. P., G. B. Hall, C. Ware, and R. B. Hupalo. 1997. Water management alternatives: 

effects on lake levels and wetlands in the Orange Creek Basin. Appendices. Special 

publication SJ97-SP8. St. Johns River Water Management District. 

Roehl, J. W. 1962. Sediment source areas, delivery ratios, and influencing morphological 

factors. International association of Scientific Hydrology 59: 202-213. Symposium of Bari, 

October 1-8, 1962. 

Schaus, M. H., M. J. Vanni, T. E. Wissing, M. T. Bremigan, J. E. Garvey, and R. A. Stein. 1997. 

Nitrogen and phosphorus excretion by detritivorous gizzard shad in a reservoir ecosystem. 

Limnology and Oceanography 42: 1386–1397. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 74

Sloto, R. A., and M. Y. Crouse. 1996. HYSEP: A computer program for streamflow hydrograph 

separation and analysis. U. S. Geological Survey Water Resources Investigations Report 96-

4040. 

St. Johns River Water Management District. 2002. Assessment of pollution sources in the 

Newnans Lake watershed. 99-0128.000/Report/TOC.Doc. 

Stites, D. L., M. Coveney, L. Battoe, E. Lowe, and V. Hoge. 2001. An external phosphorus 

budget for Lake Apopka, 1989–1994. Palatka, Florida: Division of Environmental Sciences, 

Department of Water Resources, St. Johns River Water Management District. 

User’s Manual: Watershed management model, Version 4.1. 1998. Rouge River national wet 

weather demonstration project. Wayne County, Michigan. PRO-NPS-TM27.02. 

U. S. Environmental Protection Agency. 1999. U. S. Environmental Protection Agency. 

1999. Protocol for developing nutrient TMDLs. Washington, DC: Office of Water. EPA 

841-B-89-007. 

Viessman, W., Jr., G. L. Lewis, and J. W. Knapp. 1989. Introduction to hydrology. 3rd edition. 

New York: Harper Collins. 

Walker, W. W. 1999. Simplified procedures for eutrophication assessment and prediction: 

User manual. Instruction Report W-96-2. Washington, D. C. : U. S. Army Corps of Engineers. 

Wetzel. 2001. Limnology: Lake and River Ecosystems. Third Edition. Academic Press 
75 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Appendices 

Appendix A: Background Information on Federal and State 

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 Chapter 62-40, F.A.C. 

The rule requires the state’s water management districts (WMDs) to establish stormwater 

pollutant load reduction goals (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. To date, stormwater PLRGs have been 

established for Tampa Bay, Lake Thonotosassa, the Winter Haven Chain of Lakes, the 

Everglades, Lake Okeechobee, and Lake Apopka. No PLRG had been developed for Newnans 

Lake at the time this report was developed. 

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. 

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 the FDOT throughout 

the 15 counties meeting the population criteria. 

An important difference between the federal and state stormwater permitting programs is that 

the federal program covers both new and existing discharges, while the state program focuses 

on new discharges. Additionally, Phase 2 of the NPDES Program will expand the need for 

these permits to construction sites between 1 and 5 acres, and to local governments with as few 

as 10,000 people. The 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. The Department recently accepted 

delegation from the EPA for the stormwater part of the NPDES Program. It should be noted that 

most MS4 permits issued in Florida include a re-opener clause that allows permit revisions to 

implement TMDLs once they are formally adopted by rule. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 76

Appendix B: Paynes Prairie Elevation, Area, and Volume Information 
77 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 78
79 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Appendix C: Responses to Comments 

April 6, 2005 

Mr. Daryll Joyner, P.E. 

TMDL Program Administrator 

Florida Department of Environmental Protection 

2600 Blair Stone Road, MS: 3510 

Tallahassee, FL 32399-2400 

RE: Nutrient Total Maximum Daily Load (TMDL) for Alachua Sink TMDL, February 24, 2005 

 Stakeholder Comments 

Dear Mr. Joyner: 

In response to our telephone conference held on March 28th, 2005, the following are Gainesville Regional 

Utilities’ comments on the referenced TMDL. As indicated, GRU is generally accepting of the total 

maximum daily load for Alachua Sink calculated in the revised TMDL dated February 24, 2005. However, 

we request the Florida Department of Environmental Protection (FDEP) address the following comments 

before finalizing and moving forward with the Basin Management Action Plans (BMAP) for the Alachua 

Sink. We are specifically concerned about the equitability of load allocations between non-point source 

and point source inputs. We appreciate FDEP’s previous efforts to analyze and incorporate local 

stakeholder input into the TMDL development. 

General Comments 

1. The Alachua Sink (Sink) water body is complex. FDEP’s model is limited to steady state 

scenarios, and does not adequately predict a key component of the water quality criterion for 

which it was listed: Chlorophyll-a. Future assessment phases should focus on ways of improving 

our understanding of the Sink’s hydrodynamics and response to nutrient inputs. Future TMDL 

analyses should be conducted that incorporate more sophisticated analysis of transient 

conditions in the waterbody and the upstream watershed. 

Response: We concur that the Alachua Sink waterbody is complex and work that furthers our 

understanding of the sink’s hydrodynamic and response to nutrient inputs would be beneficial. 

This is also true in the larger context of surface water/ground water interactions. An increasing 

number of springs in the state have increasing levels of nitrates, and there is a real concern 

regarding surface water impacts associated with these springs, as well what actions will be 

necessary to limit further degradation of the ground water basin.

2. The load allocation methodology is not equitable and runs counter to FDEP policy. A pound of 

total nitrogen from a non-point source is not equal to a pound of total nitrogen from the Main 

Street Water Reclamation Facility (MSWRF) in the TMDL allocation. The distribution of load 

reductions is such that the MSWRF, which currently provides approximately 19% of the TN load, 

is assigned a 65% reduction, while the Alachua Lake subwatershed, which provides 

approximately 67% of the current TN load, is assigned a 44% reduction. If the allowable load for 

MSWRF is applied to the permitted capacity of 7.5 mgd and an estimated total nitrogen effluent 

concentration of 5.0 mg/l, the current allocation results in a 73% reduction to MSWRF. We feel 

that this is inconsistent with past guidance from FDEP (A Report to the Governor and the 

Legislature on the Allocation of Total Maximum Daily Loads in Florida, FDEP 2001) that 

indicates that all anthropogenic loads would be reduced equally during the initial allocation when 

loads from non-point sources could not achieve the TMDL (see Section 4.2.3, p. 24-25 of above 

referenced document). In addition, Section 4.2.4, Item 6 (p. 27) of the referenced report indicates 

that the percent load reductions in the allocation process will consider the full permitted load for 

the existing wastewater facility. Based these guiding principles established by FDEP for load 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 80

allocations, the percent reductions for the Alachua Sink TMLD should be applied equally among 

sources and this equal percent reduction should be applied to the full permitted capacity of 

MSWRF rather than the current load condition. This proposed allocation strategy recognizes the 

prior investments in best available treatment technologies that have been made by traditional 

point sources such as the MSWRF. As an example of our prior investments, GRU spent over 

$13 million in upgrading the MSWRF in the early 1990s. This upgrade was solely to meet water 

quality based effluent limits set by FDEP and was not related to plant expansion. 

For all the specific detail that is provided regarding the BATHTUB and WMM modeling, there is 

little information that is disclosed for the load allocation methodology employed in establishing 

load reductions. It is curious why FDEP’s current approach of converting anthropogenic landuse 

to natural conditions is not yielding a higher reduction in total nitrogen when compared to the 

reductions achieved in total phosphorus with this method. 

Response: First, based on the Department’s efforts to address comments raised by GRU and the 

city, the TMDL reductions have changed and differences between the point source and nonpoint 

source required reductions are smaller. Second, the allocation guidance that was cited focused 

on “leveling the playing field,” particularly in areas where very little implementation of stormwater 

controls has occurred. The guidance was particularly toward areas that had multiple surface 

water dischargers with varying degrees of treatment and a combination of MS4 or other 

stormwater-regulated and nonregulated activities. In this case, Sweetwater Branch is an effluentdominated stream that discharges into a sink. In fact, Sweetwater Branch was on the 1998 

303(d) list based on elevated nutrient levels. The Sweetwater Branch watershed is highly 

urbanized and is part of an MS4. Nonregulated stormwater type activities do not appear to be 

significant in this watershed. Alachua Lake is the other major source contributing to Alachua 

Sink. Alachua Lake receives drainage from the city of Gainesville from the Bivans Arm area as 

well as the Newnans Lake watershed via a flow diversion from Prairie Creek. Alachua Lake is 

part of the Paynes Prairie Preserve and there is a long-term restoration strategy for that system. 

Third, the process used was based on the fact that reductions from the existing condition were 

necessary; consequently, the existing characteristics of the Main Street WWTF discharge 

became the starting point. Presumably, starting with the permitted discharge flow would have led 

to a similar result. Based on previous conversations, it appeared that efforts to reduce nitrogen 

levels were most successful when inflows were limited to about 5 mgd. Fourth, as noted prior 

investments should be taken into consideration. As part of the Orange Creek Basin BMAP team, 

the Department’s staff have worked with all the stakeholders to try and develop summaries of 

completed, current, and proposed projects by both the point source and nonpoint stakeholders 

that quantify costs as well as pollutant reductions. Based on some recent projects, there has 

been a considerable investment to reduce and improve stormwater in the basin. 

 

3. The load allocation to Alachua Sink is directly affected by the achievement of the Newnans Lake 

nutrient TMDL. The required total nitrogen load reduction for Newnans Lake, 243,260 lbs/yr, 

should be explicitly stated in the Alachua Sink TMDL to give the reader a better understanding of 

the total reductions necessary from all contributing sources for the Alachua Sink TMDL to be 

achieved. As an example of the relative impact of different sources, removing all of MSWRF’s 

nitrogen load from Alachua Sink only achieves a 10% reduction in total nitrogen concentrations in 

Alachua Sink. 

Response: The influence of implementing other TMDLs in the Orange Creek Basin such as the 

Newnans Lake nutrient TMDL will be added to the document. 

4. For the BATHTUB calibrations, FDEP had access to inflow and water quality data collected by 

Jones Edmunds & Associates, Inc. (JEA) between February 2003 and September 2004. There 

were eight sampling events in 2003 and three in 2004. For calibration of the dry weather 

scenario, FDEP chose only 2 events with which to calibrate the Alachua Lake model, citing both 

inflow and concentration variations in the other events as reasons for their exclusion. 

Investigation of the 2003 Alachua Lake data indicates that lake levels were consistently between 
81 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

55 and 56 feet from March through October of 2003. Water column nutrient concentrations for 

the October sampling event were very low, and the presence of floating macrophytes was also 

noted at the time. It is expected that water column nutrients were depleted by the macrophytes. 

This is an appropriate reason to exclude the October sample from the process of characterizing 

typical water quality for 2003. However, three other events from March to early May were also 

excluded, based on the continuously decreasing nutrient concentrations that were observed over 

those dates. FDEP speculated that these changes occurred due to the dissolution of sediment 

nutrients back into the water column, immediately after a rapid increase in the lake level. While 

this may have occurred, the maximum observed Alachua Lake TN loads over the 5 samples were 

just 25% greater than the observed TN loads from the 2 sampling dates used by FDEP. Given 

the relative stability of Alachua Lake elevation levels between March and June, the nitrogenlimited nature of Alachua Lake in early 2003, and the direct hydraulic linkage between the Lake 

and the Sink (another historically N-limited water body), the observational data from all five 

samples within the March-June time frame should be used to re-calibrate the 2003 scenario. 

For 2004, FDEP used all three sampling events to characterize the Alachua Lake and Alachua 

Sink water bodies. Based on the total observed inflow for 2004 (close to the 75th percentile), the 

year was classified as a wet year. Unfortunately, two of the three sampling events documented 

very dry conditions, especially for Alachua Sink. The third sampling event occurred in 

September, after a major hurricane event had passed through Gainesville. As such, all three 

sampling events represent extreme conditions and the average of the three events is not 

indicative of a wet year. For 2004, characteristic hydraulic and water quality conditions of the 

Lake and the Sink would be better estimated from numerical relationships associated with inflow. 

Response: A similar comment was made in the detailed comments attachment and a response is 

provided there. It is worth noting that the TN average for all the samples in 2003 was 1.94 mg/L 

and the May–June sample mean was 1.90 mg/L. The predicted value from the model was 1.94 

mg/L. With respect to the 2004 dataset, additional nutrient data was provided by ACEPD and is 

included in the report. 

5. The selection of 2003 and 2004 as representative of dry and wet conditions appears to be 

reasonable based on the total inflows recorded for those years and their comparisons to historical 

flow records. However, it should be noted that the Alachua Sink BATHTUB calibrations for those 

years were conducted for the exact same set of Alachua Sink dimensions (surface area = 70,000 

m2

, mean depth = 2.2 m). This is counterintuitive, since one would typically expect lake volumes 

to be greater during wet years than during dry years. The simulations for Alachua Sink current 

conditions are even more confusing; with the dry year mean depth set at 2.1 m and the wet year 

mean depth set lower at 1.4 m. These dry year and wet year depths were also carried through 

for the load reduction scenarios. While the source of the 2003 (dry year) mean depth is unknown, 

Table 29 in the TMDL document shows the 1.4 m value as the 2004 mean depth. Table 30 

presents alternative mean depth calculations of 2.32 m (2003) and 1.86 m (2004). While the 

2003 mean depth is based on 8 sampling events, the 2004 depth is based on only three. Each of 

the three 2004 samples represent extreme volumetric conditions in Alachua Sink, with the first 

two collected at low elevations of approximately 49 and 42 feet and the last collected shortly after 

2 hurricanes had passed through Gainesville. The Sink elevation for that sampling event was 

recorded as slightly less than 58 feet. As a result of the small sample set, the wet year volumetric 

data for Alachua Sink is essentially skewed to the sample dates when Sink dimensions were 

more representative of lower flows. Based on the estimated lake dimensions and annualized 

inflows, the residence times were 0.78 days and 0.72 days, respectively. As for the respective 

dry and wet year mean depths, this is also counterintuitive, and suggests that, as inflows to 

Alachua Sink increase, outflows increase at a higher rate, leaving less proportionate storage in 

the water body. The TMDL document also discusses a methodology for predicting lake 

elevations based on inflow (Figure 7). This was originally done to fill in elevation data gaps for 

the 2000-2002 period, when FDEP was considering using the average of those years as the dry 

year critical condition. While the linear relationship established was somewhat simplistic, the 

concept of using estimated elevations is reasonable, and would also provide the rationale for 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 82

estimating 2004 Sink dimensions, rather than relying on the skewed set of sample observations. 

Rather than using a linear relationship, we recommend a logarithmic relationship to eliminate over 

predicting stage at higher flow regimes. 

Based on additional information from ACEPD and elevation observations outside the specific 

sampling dates, refined estimates of water depth, volume, and surface area were obtained. Note 

that the elevation of 42 ft was in error and subsequently corrected by JEA. In 2003, 9 values 

were used to establish elevations, surface areas, and volumes for Alachua Lake. There were 17 

values in 2004. Similarly, 12 values were used for Alachua Sink in 2003 and 6 in 2004. 

6. Given the wet year–dry year approach for developing the TMDL and the differences in the Sink 

between these flow regimes, we recommend independent calibrations of the wet year and dry 

year conditions rather than a “one size fits all” approach. This essentially means developing and 

applying different calibration factors between wet and dry years to improve the model’s 

predictions. The calibration factors for Alachua Sink are applied to concentrations where as the 

calibration factors applied to Alachua Lake are more ambiguous in the text and are applied to the 

decay rates. We recommend a consistent approach that applies the calibration factors to 

concentrations. 

By consistently applying calibration factors to absolute concentrations, creating unique sets of wet 

and dry year calibration factors, and revising hydraulic dimensions to be reflective of varying 

annualized conditions, improvements in TN predictions can be realized for every scenario. 

Attached are comments that address specific sections of the TMDL document. As stated earlier, we have 

several concerns with regard to the model. Given the limitations of available data and time and our ability 

to re-visit the TMDL in coming basin cycles, we are generally accepting of the calculated total maximum 

daily load for the waterbody. However, we feel that the proposed load allocation is not equitable and is 

not consistent with FDEP’s policies. We appreciate FDEP’s efforts on the TMDL and look forward to the 

BMAP process. If you need any additional information, please contact me at 352-393-1613. 

Response: Several of these items are specific comments in the attachment and responses can 

be found there. 

Sincerely, 

Brett Goodman, P.E. 

Attachments: Specific Comments 

ec: Mary Paulic, FDEP 

Wayne Magley, FDEP 

 Terry Pride, FDEP 

 Fred Calder, FDEP 

 Jeff Martin, FDEP 

 Jennifer Eason, USEPA 

 Carol Lippincott, SJRWMD 

Jim Weimer, PPPS 

 Chris Bird, ACEPD 

 April Grippo, ATM 

 Bill Saunders, ATM 

Brett Cunningham, JEA 
83 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

Alice Rankeillor, CGPW 

 Sally Adkins, CGPW 

David Richardson, GRU 

Kim Zoltek, GRU 

Rick Hutton, GRU 

Paul Davis, GRU 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 84

Attachment #1 

Alachua Sink TMDL 

GRU Specific Comments 

a. Throughout the document, the use of the expression “the lake” to describe Alachua Sink is 

confusing, especially when used in describing any hydraulic connection or loadings from the 

adjacent Alachua Lake. While standard protocol at FDEP may be to refer to the water body 

under analysis as “the lake”, this document would be much clearer if all references to “the lake” 

were changed to “the sink”. 

Response: References to “the lake” have been changed to “Alachua Sink”. 

b. Section 2.1, end of first paragraph, “Quarterly TN, TP, Chl a, and TSI values were then used to 

calculate annual mean values.” This description should specifically state whether the calculated 

annual values are the mean of the quarterly values and whether that approach applies for the 

annual TSI values, also. 

Response: Annual mean values for TN, TP, chla, and TSI represented the mean of the quarterly 

averages. 

c. Table 1 and 2, the TSI values in these tables don’t appear to have been calculated using the 

Florida TSI methodology documented on page 36. The document should be specific about how 

these TSIs were determined. 

Response: The values calculated in Table 1 follow the procedure on page 36 and are described 

in Section 2.1. Attached is the spreadsheet that documents the values presented in Table 1. The 

section indicates that the model does not provide quarterly average concentrations for TN, TP, 

and chla. In Table 2 the quarterly averages for each year for 2000 to 2002 are presented and 

illustrate the degree of seasonal variation in these parameters over this period. 

Color TN TP TN/TP Chla Chla-TSI TN2-TSI NUTRTSI TSI 

CPU (mg/L) (mg/L) (μg/L) 

2000 1st Quarter 20 4.055 0.726 5.585 27.2 64.38 89.70 89.70 77.04 

2nd 

Quarter 10 3.455 0.848 4.073 41.5 70.46 86.26 86.26 78.36 

3rd Quarter 20 2.987 1.383 2.160 107.1 84.10 83.13 83.13 83.62 

4th Quarter 35 7.552 1.772 4.262 9.3 48.99 103.07 103.07 76.03 

2001 1st Quarter 15 7.222 1.436 5.030 6.9 44.66 102.11 102.11 73.38 

2nd 

Quarter 37 3.804 1.056 3.603 75.3 79.04 88.33 88.33 83.68 

3rd Quarter 450 4.412 1.570 2.810 36.0 68.41 91.51 91.51 79.96 

4th Quarter 197 3.858 1.348 2.862 14.6 55.41 88.63 88.63 72.02 

2002 1st Quarter 28 3.916 1.874 2.089 45.6 71.82 88.95 88.95 80.38 

2nd 

Quarter 20 2.521 0.841 2.999 81.4 80.14 79.48 79.48 79.81 

3rd Quarter 287 3.850 1.448 2.659 8.0 46.83 88.58 88.58 67.71 

4th Quarter 160 4.330 1.047 4.137 36.9 68.75 91.11 91.11 79.93 
85 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

d. Table 2d: It is unclear how the annual mean TSI value was calculated in this table. The TSI 

value calculated from the annual mean TN, TP, and Chl-a values from the previous three tables is 

63. The document should be specific about how this TSI was determined. 

Response: 2003 Average TN = 2.779 mg/L (31 samples) Average TP = 0.631 mg/L (31 

samples) 

 Average chla = 8.15 μg/l (31 samples) TN/TP = 4.40 

 TSICHL = 47.01 TSINUT = 81.57 TSI = (TSICHL + TSINUT )/2 = 64 

 There is a note below Table 2d describing the calculation of the annual mean TSI value. 

e. Table 2h: Contrary to the note, the annual mean value IS the simple mean of the individual TSI 

values. The TSI value calculated from the annual mean TN, TP, and chla values from the 

previous three tables is 70. 

Response: Table 2e average TN = 2.071 mg/L (13 values); Table 2f average TP = 0.677 mg/L 

(13 values) 

 Table 2g average chla = 29.77 ug/l (13 values) TN/TP = 3.59 

 TSICHL = 65.66 TSINUT = 75.25 TSI = (TSICHL + TSINUT )/2 = 70 

 There is a note below Table 2h describing the calculation of the annual mean TSI value.

f. Section 3.0, last sentence: “impact of changes in TP loading was also estimated”. There is no 

discussion in this document about the impact of changes in TP. It isn’t until the % reductions are 

disclosed in Table 45 that there is any mention of TP reductions. Discussions with FDEP 

personnel have indicated that, rather than pursuing targeted TP decreases, the identified TP 

reductions are completely due to the nonpoint source management practices applied for the TN 

reduction scenarios. This should be made clear in the document. Also, since the system is so 

highly N-limited, the TP concentrations should not affect the TSI (i.e. the calculated TSINUT value 

is based on TN concentrations only). 

Response: Since nitrogen has been identified as the limiting nutrient, this TMDL will be based on 

nitrogen. Modeling tools used in the TMDL process provide estimates of both total nitrogen and 

total phosphorus. Summary tables for both will be included in the report as appropriate to provide 

a more complete view of nutrient dynamics in the watershed. 

g. Section 4.2, last paragraph: It appears that permitted NPDES stormwater discharges are 

included in both the point source and nonpoint source analyses. The document should clarify 

how the allocated NPDES stormwater load reductions are not accounted for twice. 

Response: Text has been added in Section 6.1, and Attachment A describes the responsibilities 

for stormwater management under state and federal regulations. 

h. Section 4.4, page 15, bottom of page: The 2005 TMDL states, “To estimate TN and TP loadings 

into the Lake from Alachua Lake, the discharge from Alachua Lake into the Lake and TN and TP 

concentrations of the discharge were required. However, these data were not available for the 

period from 2000 – 2002. To estimate water quality in Alachua Lake, the WMM was used to 

evaluate how the land use pattern of the watershed area (AL) influences the water quality 

of Alachua Lake. The WMM (calibrated using the USGS gauging station) applied to the entire 

AL watershed to estimate the nonpoint flow and TN and TP loadings into Alachua Lake.” Again, 

it is unclear whether the author meant to substitute “the Lake” for Alachua Sink in the 2005 

TMDL. 

Response: Text has been modified to distinguish between Alachua Lake and Alachua Sink. 

i. Section 4.4, page 17 & Table 4: there’s no “seasonal variation” that can be derived from Table 4. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 86

Response: Reference to seasonal variation has been deleted. 

j. Section 5.3, page 38 (Data Required for Alachua Lake concentrations): the referenced lake 

characteristic curve (Robison 97) should be included with a figure or table here. 

Response: Appendix B has been added to the document; it includes capacity curves and 

elevation/surface area information. 

k. Section 5.3, Table 23: equivalent tables for the other simulated years should be included. 

Response: Tables have been added for 2004. 

l. Section 5.3, Table 23, note b: “by the total flow created in the watersheds” should be replaced 

with “by the individual flows associated with each source.” 

Response: Text changed. 

m. Section 5.3, Table 23, note c: It should be specified how much (i.e. what percentage) of the 31.6 

hm3

/yr assigned to Prairie Creek comes from the Newnans Lake diversion. 

Response: The footnote indicates that approximately 41% of the flow leaving Newnans Lake is 

diverted to Paynes Prairie. That percentage was applied to the annual flow records from the 

Prairie Creek gauge. 

n. Section 5.3, Table 24: The use of only the 5/22/03 and 6/9/03 observations for calibration of the 

Alachua Lake model creates a system imbalance that overestimates the N loadings received from 

other subwatersheds (i.e. Sweetwater Branch, direct runoff) to Alachua Sink. For these two 

samples, the N/P ratio is in the 13-15 range, significantly above the generally assumed value of 4 

for Alachua Sink. This characterization of Alachua Lake as co-limited, combined with an Alachua 

Sink characterization as N-limited, is dubious, considering their proximity and direct linkage. As 

can be seen from Figure 6 and from JEA’s Phase 1 and Phase 2 loading study data, the lake 

elevation values for Alachua Lake were between 55 and 56 feet (NGVD) for every sampling event 

between March 12, 2003 and October 16, 2003. FDEP makes a significant point regarding 

exclusion of the October sampling event, due to the presence of floating aquatic plants at the 

time. However, the exclusion of the March and early May events, due to the potential for 

elevated nutrient levels from previously oxidized nutrients in the inundated sediment, is primarily 

based on conjecture. Conversely, inclusion of the samples from March and May lead to TN and 

TP averages of 2.21 and 0.49 mg/L, respectively (representing an N/P ratio of approximately 4.5). 

Given what is known about the trophic state of Alachua Sink and the relative stability of Alachua 

Lake elevation levels between March and June, observational data from all samples within that 

time frame should be used to re-calibrate the 2003 scenario. 

Response: Table 25 summarizes observations and model predictions of TN and TP for Alachua 

Lake in 2003. The May–June average TN was 1.901 mg/L, while the average of all samples 

collected in 2003 was 1.941 mg/L. The model prediction was 1.945 mg/L. As noted, the greatest 

difference occurred in TP, where the May–June average was 0.14 mg/L and the average over the 

year was 0.41 mg/L. The average was high due to values above 1 mg/L in February and March. 

Historical data for Florida streams and lakes have median TP concentrations of 0.08 mg/L and 

0.04 mg/L, respectively. Although the median TP for Alachua Lake in 2003 (0.14 mg/L) was 

elevated compared with these medians, it was much more representative of the year compared 

with the mean. With respect to the comment that due to their proximity and direct linkage it 

dubious that Alachua Sink and Alachua Lake could reflect different nutrient limitations, the 

statement may be true in general, but one must also consider whether different types of sources 

contribute to the waterbodies. Certainly a waterbody receiving a discharge from a domestic 

wastewater facility that typically is nitrogen limited can have a significant influence on what 

nutrient might be limiting. 
87 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

o. Figure 6 should encompass the monitoring performed in 2004 to provide additional information on 

the nitrogen and water level fluctuations in the sink and to check the validity of using only May 22 

and June 9, 2003 as calibration points. 

Response: Figure 6 illustrated sampling and loading estimates for 2003. Each year was run 

separately. Table 27 was added to provide information on TN and TP measurements in 2004. 

Unfortunately, flow measurements were available for only three dates in 2004. 

p. Section 5.3, Table 26: 2004 calibration of the Alachua Lake Bathtub model is given light 

treatment in the text, especially in comparison to the discussion provided for the 2003 calibration. 

Although 2004 surveys by JEA and the Alachua County Environmental program are referenced, 

there is no analysis of that sampled data and how it relates to the calibration. TN and TP are 

significantly under predicted, compared to the 2003 calibration. Since the point source 

discharges are relatively well quantified via DMR data for all years, one would suspect that this 

under prediction is associated with the nonpoint source load received by Alachua Lake. 

Response: Tables have been added for 2004 that include sampling data and model estimates of 

flow from various sources. Part of the difficultly in 2004 was the limited set of flow measurements 

and elevations. During the spring and summer there was a steady decline in water level 

elevation at Alachua Sink and Alachua Lake. Each of the months from March–July was below 

average in rainfall, and then August had 14.32 inches, followed by 16.45 inches in September. 

Nearly 58% of the total rainfall for 2004 occurred in the August (24.6%) and September (28.2%). 

As a consequence, there were large fluctuations in the size and volume of Alachua Lake. 

q. Section 5.3, page 43 (simulation of TN, TP for Alachua Lake 2000-2002): Table 27 is incorrectly 

referenced as Table 26. 

Response: Table numbers have been corrected. 

r. Section 5.3, Multiple Tables have values which do not match up with the bathtub input files: 

• Table 21: Lake Surface Area in the 2004 year does not match up with the physical 

characteristics surface area value in the as2004.btb bathtub file. 

• Table 22: Evaporation in years 2001-2002 do not match up with the evaporation 

• values in the Bathtub input files (as2001.btb and as2002.btb) 

• Table 29: Most of the values in this table do not match up with the physical characteristics in 

the Bathtub input files (i.e. as2000.btb – as2004.btb) 

• Table 35: The TP value for Main Street WWTP is listed as 1.19, however it is .89 in the 

bathtub file, as202122.btb. 

• Table 36: The TP and TN values for Main Street WWTP do not match up exactly with the 

bathtub file, as2003.btb 

• Table 37: The TP and TN values for Main Street WWTP do not match up with the bathtub file, 

as2004.btb 

 Response: Bathtub files have been revised. 

s. Section 5.3, Table 31: The bathymetry data in this table doesn’t go high enough to accommodate 

determination of Alachua Sink volume and surface area for 2003 or 2004. 

Response: The table summarized bathymetry data provided by JEA based on a field study. The 

data were curve fit to predict volume and surface area for elevations above 52 ft. 

t. Section 5.3, page 49, paragraph after Table 37: “The septic tank fluxes were calculated as 

previously described.” The source of the annualized septic tank loading data (and preferably the 

loading values), for which these fluxes were calculated, should be identified here. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 88

Response: Items H and I describe the procedure used in WMM to estimate loadings from septic 

tanks. The following table summarizes the TN and TP loadings by year and drainage area. 

Septic Tank 

Loadings 

Upper 

Sweetwater 

Branch 

Lower 

Sweetwater 

Branch 

Upper 

Extension 

Ditch 

Alachua 

Sink 

Watershed 

Paynes 

Prairie 

Total 

TN (lbs/yr) 

2000 1344.4 1328.1 152.6 3.7 4810.4 

2001 1647.4 1627.4 186.9 4.5 5894.4 

2002 2163.0 2136.7 245.4 5.9 7739.4 

2003 1822.5 1800.4 206.8 5.0 6521.1 

2004 2280.2 2252.6 258.8 6.2 8159.0 

TP (lbs/yr) 

2000 477.0 448.0 52.0 0.1 1700.3 

2001 584.5 549.0 63.7 1.2 2083.4 

2002 767.5 720.8 83.6 1.5 2735.5 

2003 646.7 607.4 70.4 1.3 2304.9 

2004 809.1 759.9 88.1 1.6 2883.9 

u. Section 5.3, page 49-50, Calibration Factors: The calibration factors for Alachua Sink are based 

on concentration and are discussed in the write-up. However, there is no commensurate 

discussion of the Alachua Lake calibration factors. A review of the Alachua Lake Bathtub input 

files shows that those calibration factors are based on decay rates and not concentrations. We 

recommend a consistent approach that applies the calibration factors to concentrations. Also, 

while the Alachua Sink TN and TP calibration factors are set at 1.0 and 2.0, respectively, the 

Alachua Lake TN and TP factors are 1.5 and 0.9. Based on these two differences, it is not 

surprising that the TN and TP percent errors for the 2004 Alachua Lake calibration are so much 

greater than those for the 2003 calibration (table 26 vs. table 25). 

Response: Concentration factors were used in Alachua Sink since detailed information existed 

for flow and water quality characteristics of the point and nonpoint sources discharging to 

Sweetwater Branch and Alachua Sink. In contrast, very little flow, water quality input 

characteristics, or lake characteristics (surface area, volume, etc.) were available for Alachua 

Lake. Therefore, calibration factors that relied more on lake processes such as decay rates (that 

had a certain range based on numerous studies) were used in Alachua Lake. The same 

calibration factors were used for Alachua Lake in the 2000–02, 2003, 2004, wet and dry 

simulations. A number of factors that could have affected the model prediction in 2004 were 

previously discussed. 

v. Section 5.3, Page 50, Table 38 and discussion: The annual averages of observed TP 

concentrations referenced in the paragraph (for 2000, 2002, and 2004) do not match the 

measured values in the table and would change the calibration results from “consistent under 

prediction” to “over predicted in 2000, close to observed in 2002, and under predicted in 2004”. 

Also, the 2004 annual averages of both TN and TP don’t appear to be calculated from the JEA 

and ACEPD data. The document should be specific about how these measured values were 

calculated. 

Response: The table has been corrected. Tables 2e, 2f, and 2g summarize the JEA and ACEPD 

data collected in Alachua Sink. The middle station represents measurements by ACEPD. 

Annual averages were calculated by summing all the observations in the respective table and 
89 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients

taking the average. A table was also added with JEA and ACEPD TN and TP measurements for 

Alachua Lake in 2004. 

w. Section 5.3, Page 53: last paragraph: tua0 values do not match those referenced on page 51 and 

elsewhere in the text. 

Response: The text has been revised along with some changes based on additional calculations. 

x. Section 5.3, Page 57, (evaluation of Alachua Sink background TSI), first bullet: statement does 

not include the anthropogenic land use categories in the watershed draining directly to Alachua 

Sink. 

Response: The text has been modified to indicate that the analysis considered direct drainage to 

Alachua Sink. 

y. Section 5.3, Page 57, (evaluation of Alachua Sink background TSI), last bullet: the justification or 

basis for the additional Prairie Creek TN concentration reduction (1.2 mg/L from the Newnans 

Lake TMDL to 0.88 mg/L) should be explicitly identified in this section. 

Response: Text has been added to indicate that there was a consistent reduction in TN 

concentrations based on monthly monitoring at two stations in Prairie Creek. The mean percent 

reduction was applied to the TN TMDL target value for Newnans Lake. 

z. Section 5.3, Tables 40 and 41: The notes for these tables are in error with respect to TN and TP 

concentrations listed in Table 39. There are no TN and TP concentrations in that table. Also, the 

flows in table 39 from Alachua Lake to Alachua Sink do not match up with the flows quoted in the 

paragraph preceding Table 40. 

Response: Text and tables have been corrected. 

aa. It should be noted that the wet year septic loadings in Table 44 appear to be in error, since they 

are shown as only 20% of the dry year loads. GRU estimates that the corrected wet year septic 

loading should be 29,209 lbs/yr (resulting in a corresponding adjustment of the total wet year load 

to 530,902 lb/yr). This estimate was calculated from the internal load TN flux information and 

surface area in the aswetcur.btb input file. The total TN load was also adjusted to accommodate 

the revised septic load. 

U. S. Environmental Protection Agency. 1999. Protocol for developing nutrient TMDLs. 

Washington, DC: Office of Water. EPA 841-B-89-007. 

bb. Section 5.3, Page 60, Critical Conditions: reference to table 45 should be table 44. 

Response: Text has been changed. 

cc. Section 5.3, Page 62??. Page numbers skip from 61 to 63. Is there actually a page 62 that is 

missing from the document?? 

Response: Page 62 was blank and was due to a formatting problem changing from landscape to 

portrait. 

dd. The document should provide tables in Section 5.3 consistent with table 18 and 19 that show the 

reduced loads from non-point source inputs. 

Response: Table 45 in the earlier report was intended to summarize allowable point and 

nonpoint source loadings that would achieve the TMDL target. 
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 90

ee. Section 5.3, Page 63, top paragraph: 

• “TN and TP loadings during the dry year were reduced until a TSI of 63 was achieved”. This 

value should be 69 (or 68.95). 

• Also, there is no discussion about how the relative TN and TP reductions were implemented. 

Based on the percent reductions in Table 45, they were not done equally. 

• A reconciliation between the 65% TN reductions quoted in the paragraph and the 50% 

reductions identified in Table 45 is warranted. 

• The allowable TN loading of 31, 057 lbs/yr quoted in the paragraph appears to be for the 

Main Street WWTF only. It should include all point sources. 

• Table 45 is incorrectly referenced as table 46. 

Response: The text has been corrected. Reductions were based on a uniform reduction in 

human-influenced land uses. The difference between nitrogen and phosphorus responses has to 

do with the differences in EMC values of the specific land uses and runoff differences. Separate 

loads of nitrogen have been allocated to the two permitted point sources (Main Street WWTF and 

John R. Kelly Generating Station) and are specified in the document. 

ff. Input files: The wet and dry “current” scenarios for Alachua Lake mistakenly have the Prairie 

Creek TP input concentration as 0.88 mg/L. The value should be 0.16 mg/L, in accordance with 

Table 23 and the calibration input files. 

Response: Input files have been corrected. 

gg. In Table 46, it appears that the LA load allocation is double counting the NPDES stormwater 

allocation. If one subtracts the LA from the TMDL, the result is approximately the wastewater 

portion of the load allocation which leaves no allowable load for the NPDES stormwater source 

(249,612 – 217,754 = 31,858 lb/yr). From Table 45, it appears that the LA in Table 46 should be 

195,090 lbs/yr. Section 6.1 on page 66 should be revised to reflect the revised LA load allocation 

number. 

Response: Table 46 is confusing in that the LA value really represents the complete allowable 

nonpoint source load of nitrogen from both MS4 and nonregulated areas. Text has been added 

to try and clarify this. Without specific information on MS4s, the Department has considered all of 

the stormwater loading together and used a percent reduction approach that would apply equally 

to MS4 and no MS4 areas. 

hh. The second sentence in the last paragraph in Section 6.2 on page 66 is not correct. The current 

total nitrogen loading to Alachua Sink is 413,000 lbs/yr of which 88,748 lbs/yr come from 

MSWRF, which is 21% of the loading rather than the reported 43%. 

Response: The text has been corrected. 
91 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 92
93 TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients
TMDL Report: Ocklawaha Basin, Alachua Sink, WBID 2720A, Nutrients 94

Response: As discussed at the March 28, 2005 teleconference, the sub-basin identified as 

Alachua Sink represents the original delineation of 120.24 acres and does not include the Calf 

Pond watershed. Figures, tables, and model simulations presented in this document reflect this 

change. 

The revised TMDL requires a 45% reduction in nonpoint source loads of total nitrogen from both 

MS4 permitted, other regulatory non-MS4, and nonregulated nonpoint source–generating 

activities. As part of the Basin Management Action Plan (BMAP) process, Department staff have 

been working with stakeholders to document and quantify recent, current, and proposed projects 

within the basin that have improved water quality. This will assist in determining what progress 

has been made toward achieving the TMDL, what remains, and how the remainder will be 

allocated most effectively. 
www2.dep.state.fl.us/water/ 

(850) 245-8561 

Tallahassee, Florida 32399-2400 

2600 Blair Stone Road, Mail Station 3555 

Bureau of Watershed Management 

Division of Water Resource Management 

Florida Department of Environmental Protection