Final 

FLORIDA DEPARTMENT OF ENVIRONMENTAL 

PROTECTION 

Division of Water Resource Management, Bureau of Watershed Management

NORTHEAST DISTRICT • SUWANNEE RIVER BASIN 

Nutrient and Dissolved Oxygen TMDL for the Suwannee River, 

Santa Fe River, Manatee Springs (3422R), Fanning Springs (3422S), 

Branford Spring (3422J), Ruth Spring (3422L), Troy Spring 

(3422T), Royal Spring (3422U), and Falmouth Spring (3422Z) 

John F. Hallas 

Wayne Magley, PhD 

9/24/08 
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Acknowledgments 

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

Department of Environmental Protection (Department) and the Suwannee River Water Management District 

(SRWMD). Throughout the several years that this project spanned, there was excellent cooperation and 

coordination between the staff of the two agencies and the Department wishes to express its appreciation to the 

SRWMD for its cooperative spirit. 

Editorial assistance provided by Drew Bartlett, Jan Mandrup-Poulsen, and Linda Lord. 

Geographic Information Systems assistance by Latrincy Whitehurst, as Latrincy prepared many of the supporting 

figures in the document. 

For additional information on the watershed management approach and impaired waters in the Suwannee River 

Basin, contact 

Terry Hansen 

Florida Department of Environmental Protection 

Bureau of Watershed Management 

Watershed Planning and Coordination Section 

2600 Blair Stone Road, Mail Station 3565 

Tallahassee, FL 32399-2400 

Email: Terry.Hansen@dep.state.fl.us

Phone: (850) 245-8561; SunCom: 5561 

Fax: (850) 245-8434 

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 Assessment Section 

2600 Blair Stone Road, Mail Station 3565 

Tallahassee, FL 32399-2400 

Email: Wayne.Magley@dep.state.fl.us

Phone: (850) 245-8463, SunCom: 5463 

Fax: (850) 245-8356 
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Contents 

Nutrient and Dissolved Oxygen TMDL for the Suwannee River, Santa Fe River, Manatee 

Springs (3422R), Fanning Springs (3422S), Branford Spring (3422J), Ruth Spring (3422L), 

Troy Spring (3422T), Royal Spring (3422U), and Falmouth Spring (3422Z) ............................ 1

Acknowledgments........................................................................................................................... 2

Contents.......................................................................................................................................... 3

List of Figures ................................................................................................................................ 4

List of Tables .................................................................................................................................. 5

Web sites ......................................................................................................................................... 7

Chapter 1: INTRODUCTION.................................................................................................... 8

1.1 Purpose of Report...........................................................................................................................................8

1.2 Identification of the Waterbody ....................................................................................................................8

1.2.1 Suwannee River Basin.............................................................................................................................8

1.2.2 Santa Fe River Basin .............................................................................................................................14

1.3 Background ..........................................................................................................................................................16

Chapter 2: DESCRIPTION OF WATER QUALITY PROBLEM ......................................... 18

2.1 Statutory Requirements and Rulemaking History ....................................................................................18

2.2 Information on Verified Impairment..........................................................................................................24

2.2.1 Nutrients ................................................................................................................................................24

2.2.2 Dissolved Oxygen..................................................................................................................................26

2.2.3 Sampling Sites...............................................................................................................................................28

Chapter 3: DESCRIPTION OF APPLICABLE WATER QUALITY STANDARDS ........... 33

3.1 Classification of the Waterbody and Criteria Applicable to the TMDL .................................................33

3.2 Interpretation of Dissolved Oxygen Criterion and Narrative Nutrient...................................................33

3.3 Outstanding Florida Waters Classification (OFW)...................................................................................34

3.4 Watershed Management Basin Rotation Cycle 1 ......................................................................................34

3.5 Suwannee River Partnership and Reasonable Assurance Documentation .............................................34

Chapter 4: ASSESSMENT OF SOURCES............................................................................. 35

4.1 Types of Sources ...........................................................................................................................................35

4.2 Point Sources in the Suwannee River Basin...............................................................................................35

4.2.1 Municipal Separate Storm Sewer System Permittees........................................................................40

4.3 Nonpoint Sources..........................................................................................................................................40

4.3.1 Onsite Sewage Treatment and Disposal Systems..............................................................................42

4.3.2 Human Population.............................................................................................................................43

4.3.3 Animal Operations ............................................................................................................................47

4.3.4 Agriculture ........................................................................................................................................47

4.3.5 Land Uses..........................................................................................................................................48
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Chapter 5: DETERMINATION OF ASSIMILATIVE CAPACITY ...................................... 55

5.1 Hydrology......................................................................................................................................................55

5.2 Water Quality Over Time............................................................................................................................57

5.3 Flows over time.............................................................................................................................................59

5.4 Biological Effects ..........................................................................................................................................60

5.5 Nitrate (NO3) Target ....................................................................................................................................60

5.5.1 Laboratory nutrient amendment bioassays ........................................................................................60

5.5.2 Relationship between ecological efficiency and nitrate concentration..............................................61

5.5.3 Examining the ecological condition of algae and nutrients in Florida Springs Report......................61

5.5.4 Relationship between periphyton biomass and cell density and nitrate concentration......................62

5.5.5 Target Setting. ...................................................................................................................................66

5.6 Effects of independent variables on Nitrate. ..............................................................................................69

5.7 Setting the Monthly Average Concentration for Nitrate ..........................................................................70

Chapter 6: DETERMINATION OF THE TMDL................................................................... 73

6.1 Expression and Allocation of the TMDL....................................................................................................73

6.2 Load Allocation.............................................................................................................................................75

6.3 Wasteload Allocation....................................................................................................................................75

6.3.1 National Pollutant Discharge Elimination System Stormwater Discharges ..........................................75

6.4 Margin of Safety ...........................................................................................................................................75

6.5 Recommendations for Further Studies.......................................................................................................76

Chapter 7: NEXT STEPS: IMPLEMENTATION PLAN DEVELOPMENT AND BEYOND

....................................................................................................................................................... 77

7.1 Basin Management Action Plan ..................................................................................................................77

References .................................................................................................................................... 78

Appendices.................................................................................................................................... 80

Appendix A: Background Information on Federal and State Stormwater Programs ............. 80

Appendix B Change Point Analysis of the Suwannee River Algal Data.............................. 81

Appendix C Historic Fertilizer Sales...................................................................................... 95

Appendix D Public Comments.............................................................................................. 101

List of Figures 

Figure 1.1 Suwannee Santa Fe Reaches....................................................................................................................9

Figure 1.2 Middle Suwannee Planning Unit and major cities in study area...........................................................11

Figure 1.3 Lower Suwannee Planning Unit and major cities in study area............................................................13

Figure 1.4 Santa Fe Planning Unit and major cities in study area.........................................................................15

Figure 2.1 Middle Suwannee WBIDs ......................................................................................................................21

Figure 2.2 Lower Suwannee WBIDs .......................................................................................................................22

Figure 2.3 Santa Fe WBIDs ....................................................................................................................................23

Figure 2.4 Total Phosphorus-Three Year Rolling Average by Planning Unit ........................................................25
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Figure 2.5 Rolling Average TP concentrations for the Middle Suwannee River and TP fertilizer sales for 

Suwannee and Lafayette counties................................................................................................................................25

Figure 2.6 Middle Suwannee Aerial and Sampling Station Locations ....................................................................28

Figure 2.7 Lower Suwannee Aerial and Sampling Station Locations .....................................................................29

Figure 2.8 Santa Fe Aerial and Sampling Station Locations ..................................................................................30

Figure 2.9 Photographic evidence 2000 .................................................................................................................31

Figure 2.10 Additional Photographic Evidence....................................................................................................32

Figure 4.1 Wastewater Facilities in the Middle Suwannee River Basin..................................................................37

Figure 4.2 Wastewater Facilities in the Lower Suwannee River Basin...................................................................38

Figure 4.3 Wastewater Facilities in the Santa Fe River Basin................................................................................39

Figure 4.4 Total Nitrogen inputs in the Middle Suwannee......................................................................................40

Figure 4.5 Total Nitrogen inputs in the Lower Suwannee.......................................................................................41

Figure 4.6 Total Nitrogen inputs in the Santa Fe....................................................................................................41

Figure 4.7 Onsite Sewage in the Suwannee River Basin.........................................................................................42

Figure 4.8 Middle Suwannee Basin Population Density.........................................................................................44

Figure 4.9 Lower Suwannee Basin Population Density .........................................................................................45

Figure 4.10 Santa Fe Basin Population Density...................................................................................................46

Figure 4.11 Principal land uses in the drainage basin of the Middle Suwannee River. .......................................49

Figure 4.12 Principal land uses in the drainage basin of the Middle Suwannee River. .......................................50

Figure 4.13 Principal land uses in the drainage basin of the Lower Suwannee River. ........................................51

Figure 4.14 Principal land uses in the drainage basin of the Lower Suwannee River. ........................................52

Figure 4.15 Principal land uses in the drainage basin of the Santa Fe River. .....................................................53

Figure 4.16 Principal land uses in the drainage basin of the Santa Fe River ......................................................54

Figure 5.1 Floridian Aquifer ...................................................................................................................................56

Figure 5.2 Historic Nitrate Data for the Suwannee River at Branford, FL.............................................................57

Figure 5.3 Historic Nitrate Data for the Santa Fe River.........................................................................................58

Figure 5.4 Historic Flow Data Branford FL...........................................................................................................59

Figure 5.5 Nitrates Loads from the Suwannee River to the Gulf of Mexico from 1998-2005 (Hornsby 2007).......60

Figure 5.6 Correlation between ecological efficiency and nitrate concentration in WR, RSR, ASC, and JC. ........61

Figure 5.7 Springs included in the 2007 report.......................................................................................................62

Figure 5.8 Change Point Study Sites.......................................................................................................................63

Figure 5.9 Relationship between mean nitrate concentration and mean periphyton biomass from 12 sampling 

sites on the Suwannee, Santa Fe, and Withlacoochee Rivers ......................................................................................64

Figure 5.10 Relationship between mean nitrate concentration and mean periphyton cell density from 12 

sampling sites on the Suwannee, Santa Fe, and Withlacoochee Rivers.......................................................................65

Figure 5.11 Change Point Analyses the 95% confidence interval ........................................................................66

Figure 5.12 Central Tendency and Upper 95% Confidence interval approach ...................................................67

Figure 5.13 Upper and Lower 95% Confidence Interval approach. ....................................................................68

List of Tables 

Table 1.1 WBIDs in the Middle Suwannee Planning Unit.....................................................................................12

Table 1.2 WBIDs in Lower Suwannee Planning Unit............................................................................................14

Table 1.3 WBIDs in the Santa Fe Planning Unit...................................................................................................15

Table 2.1 Cycle 2 Verified List for Suwannee River Basin ....................................................................................18

Table 2.2 Summary of DO Data by Month for the Verified Period (June 1, 2000 – June 30, 2007).....................26

Table 2.3 Summary of DO Data by Season for the Verified Period (June 1, 2000 – June 30, 2007)....................26

Table 2.4 Summary of DO Data by Year for the Verified Period (June 1, 2000 – June 30, 2007)........................27

Table 4.1 NPDES permitted facilities identified in the drainage basin discharge to Suwannee River Basin........35

Table 4.2 MS4 Permittees......................................................................................................................................40

Table 4.3 Estimated Number of Onsite Sewage Treatment Systems ......................................................................42

Table 4.4 Population and number of household in SRB ........................................................................................43

Table 4.5 Animal Operations 2007 Estimates by planning unit ............................................................................47
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Table 4.6 Total Nitrogen contribution estimates. ..................................................................................................47

Table 4.7 Acreages and percent acreages of different land use categories for the SRB........................................48

Table 5.1 Spearman Correlation on Cell Density and Biomass ............................................................................69

Table 5.2 Multiple Regression on Cell Density and Biomass................................................................................69

Table 5.3 Partial correlation on Cell density and biomass ...................................................................................70

Table 5.4 NO3 + NO2 Concentrations (mg/L) in the Main Stem WBIDs over the 1999 - 2006 period, Middle 

Suwannee River ...........................................................................................................................................................71

Table 5.5 NO3 + NO2 Concentrations (mg/L) in the Main Stem WBIDs over the 1999 - 2006 period, Lower 

Suwannee River ...........................................................................................................................................................71

Table 5.6 NO3 + NO2 Concentrations (mg/L) in the Main Stem WBIDs over the 1999 - 2006 period, Lower Santa 

Fe River 71

Table 5.7 Median NO3 in Springs within the SRB .................................................................................................72

Table 6.1 TMDL components for Suwannee River and Santa Fe River Basins WBIDs, shown as related by 

Planning Units.............................................................................................................................................................74

Table 6.2 Daily maximum for target nitrate concentration (mg/L) .......................................................................75

Table C.1 Historic Total Nitrogen Sales 1945-1991 (Tons)...................................................................................95

Table C.2 Historic Total Phosphorus Sales 1945-1991 (Tons)..............................................................................96

Table C.3 1998 to 2007 Fertilizer Sales (Tons) .....................................................................................................97
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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

Criteria for Surface Water Quality Classifications 

http://www.dep.state.fl.us/water/wqssp/classes.htm

Basin Status Reports 

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

Water Quality 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

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/
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Chapter 1: INTRODUCTION 

1.1 Purpose of Report 

This document presents Total Maximum Daily Loads (TMDLs) for Nitrate (NO3) for the Middle Suwannee River, 

Lower Suwannee River and the Santa Fe River, in the Suwannee River Basin (SRB). The river was verified as 

impaired by nutrients based on elevated chlorophyll a and photographic evidence in the freshwater and marine 

portions of the river. It was included on Florida’s Verified List of impaired waters for the SRB that was adopted by 

Secretarial Order on June 3, 2008. The purpose of this TMDL is to establish the allowable amount of pollutants to 

Suwannee River and the Santa Fe River that would restore these waterbodies such that they meet their applicable 

water quality criteria for nutrients. This report will be used as the basis for discussions during the development of 

the Basin Management Action Plan (BMAP). While the BMAP is under development, the Department recognizes 

the activities of the Suwannee River Partnership, which include the implementation of best management practices, 

significant public outreach, and advancing needed research with respect to nutrient controls, as the necessary 

implementation steps for this TMDL until such time as the BMAP discussions generate other actions that would 

provide further water quality improvements 

1.2 Identification of the Waterbody 

1.2.1 Suwannee River Basin 

The Suwannee Basin drains approximately 10,000 square miles of south Georgia and north Florida, discharging an 

annual average flow of approximately 10,000 cubic feet per second (cfs)(Figures 1.1-1.4) (FDEP 2001). The 

Suwannee River is the second largest river in the state in terms of flow. Within the Suwannee Basin, the Alapaha, 

Withlacoochee, and Upper Suwannee watersheds lie almost entirely in Georgia. These are dominated by surface 

water runoff, as are the Florida portions of the basin in the Northern Highlands region. After crossing the Cody 

Scarp, ground water discharges from springs and diffuse seepage strongly influences the Suwannee River and makes 

up the baseflow of the river. Most of the streams in the Upper Suwannee and Santa Fe watersheds are highly 

colored (blackwater). Blackwater streams typically have low dissolved oxygen (DO) concentrations and acidic, 

highly colored water and these streams are less biologically productive than some of the downstream stretches of the 

river. In the lower third of the basin, surface waterbodies are relatively absent because recharge flows directly to the 

aquifer through karst features. Along the coast, there are extensive tidal salt marshes, with hardwood swamps lying 

at slightly higher elevations just inland. Although the coastline has no barrier islands, much of this stretch is 

estuarine in nature, due to the low-energy wave action, shallow water, and fresh water inflows. Seagrass beds are 

healthy and abundant, except at the mouths of the river where seagrasses are sparse or absent due to the dark color 

of the river discharges that limit light in the area (FDEP 2001). 

The SRB contains two major physiographic regions, the Northern Highlands and the Gulf Coastal Lowlands. 

Separating the two is the Cody Scarp, a steep face that constitutes the most prominent topographic feature in the 

state. Much of the lowlands make up a karst plain where sinkholes form and natural limestone springs occur. 

Although the highlands contain some springs, most of the basin’s more than 250 springs are in the lowlands. 

Springs are especially abundant along the Suwannee River where the river has cut into the upper portion of the 

limestone bedrock. Characteristics of the marshes and swamps are typically found along the Gulf Coast. 

The Suwannee River, as is cuts through North Florida, goes through changes, as does its water chemistry. These 

changes are reflected by its’ six ecological region or reaches (Figure 1.1). 

Reach 1. Upper River Blackwater Reach 4. Lower River Calcareous 

Reach 2. Cody Scarp Transitional Reach 5. Tidal Riverine 

Reach 3. Middle River Calcareous Reach 6. Estuarine 
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Figure 1.1 Suwannee Santa Fe Reaches 

 
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The upper Suwannee River (Reaches 1 and 2) is an acidic, blackwater stream, with waters of low mineral content 

(low hardness) and high color. As the river progresses downstream (Reaches 3, 4, and 5), it receives increasing 

amounts of water from the Floridian aquifer, which changes river water quality to a clear, slightly colored, alkaline 

stream (Hornsby et al., 2000). 

These natural chemical gradients influence the ecology of the river in many ways. In terms of overall biological 

production, the upper river tends to be more oligotrophic, while the lower river is more productive. 

For assessment purposes, the Department has divided the SRB into water assessment polygons with a unique 

waterbody identification (WBID) number for each watershed or stream reach. The main stem of the SRB is divided 

into fifteen segments. WBIDs are combined into larger units called Planning Units. Figures 1.2-1.4 illustrate the 

Middle Suwannee, Lower Suwannee and Santa Fe Planning Units and Tables 1.1-1.3 list the WBIDs in each of the 

Planning Units. 
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Figure 1.2 Middle Suwannee Planning Unit and major cities in study area 
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Table 1.1 WBIDs in the Middle Suwannee Planning Unit 

WBID Name 

3422B Suwannee River (Lower) 

3422C Townsend Pond Near May 

3422J Branford Spring 

3422L Ruth Spring 

3422P Mearson Spring 

3422Q Ellaville Spring 

3422T Troy Spring 

3422U Royal Spring 

3422V Convict Spring 

3422W Running Spring 

3422X Telford Spring 

3422Y Charles Spring 

3422Z Falmouth Spring 

3438 Temnile Hollow 

3438A Peacock Lake 

3438B White Lake 

3439 Unnamed Drain 

3469 Springhead Creek 

WBID Name 

3471 Unnamed Ditch 

3472 Bethel Creek 

3476 William Waterhole Dr 

3480 Bethel Creek 

3483 Peacock Slough 

3485 Unnamed Branch 

3495 Fourmile Creek 

3496 Little River 

3496A Low Lake 

3496B Unnamed Slough 

3496Z Little River Springs 

3497 Unnamed Drain 

3498 Crab Creek 

3501 Unnamed Drain 

3502 Unnamed Branch 

3507 Unnamed Drain 

3508 Unnamed Branch 

3509 Unnamed Drain 

WBID Name 

3515 Unnamed Slough 

3521 Unnamed Drain 

3523 Thomas Spring 

3525 Allen Mill Pond 

3528 Lafayette Blue Spring Drain 

3528Z Lafayette Blue Springs 

3529 Irving Slough 

3543 Unnamed Slough 

3561 Morgan Lagoon 

3568 Owens Spring 

3591 Picket Lake Outlet 

3591A Picket Lake 

3597 Unnamed Slough 

3608 Unnamed Ditch 

3618 Unnamed Slough 

3624 Unnamed Slough 

3636 Unnamed Slough 

3643 Unnamed Ditch 
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Figure 1.3 Lower Suwannee Planning Unit and major cities in study area. 
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Table 1.2 WBIDs in Lower Suwannee Planning Unit 

WBID Name 

3422 Suwannee River (Lower) 

3422A Suwannee River (Lower) 

3422D Lower Suwannee Estuary 

3422K Guaranto Spring 

3422M Turtle Spring 

3422N Hart Springs 

3422R Manatee Springs 

3422S Fanning Springs 

3652 Sevenmile Lake Outlet 

3652A Sevenmile Lake 

3662 Cow Pond Outlet 

WBID Name 

3662A Cow Pond 

3668 Beason Prairie Drain 

3668A Govenor Hill Lake 

3673 Rock Bluff Spring 

3679 Unnamed Slough 

3684 Old Town Hammock Drain 

3687 Unnamed Drain 

3693 Unnamed Slough 

3704 Unnamed Drain 

3707 Unnamed Drain 

3708 Unnamed Drain 

WBID Name 

3709 Unnamed Drain 

3710 Unnamed Slough 

3713 Drummond Pond Outlet 

3715 Yellow Jacket Slough 

3716 Unnamed Drain 

3717 Unnamed Drain 

3722 Week Creek 

3726 Sandfly Creek 

3732 Gopher River 

3733 Direct Runoff To Gulf 

1.2.2 Santa Fe River Basin 

The Santa Fe River is a tributary to the Suwannee River (Figure 1.4). This river system drains about 1,400 square 

miles of north Florida, discharging an annual average flow of more than 1,600 cfs. The Santa Fe River flows west 

from its headwaters in the Santa Fe Lakes area, in the easternmost portion of the watershed, joining the Suwannee 

River near Branford. Its two major tributaries, New River and Olustee Creek, have their headwaters in southern 

Baker County. A third tributary, the Ichetucknee River is a clear, spring-fed stream and a very popular recreational 

site. The Upper Santa Fe watershed, in the Northern Highlands, is dominated by surface water runoff. At the Cody 

Scarp, the river goes underground and reemerges supplemented by ground water flow. As the Santa Fe flows across 

the Gulf Coastal Lowlands, it gains significant flow from numerous springs, including the Ichetucknee River. 

Because ground water dominates its flow, the Lower Santa Fe is for the most part a spring-fed river. The eastern 

two-thirds of the Santa Fe watershed has surface drainage features, including lakes, streams, and wetlands. The 

western third lacks surface drainage, except for the Santa Fe and Ichetucknee Rivers and Cow Creek. The upper 

watershed is characterized by nearly level pine flatwoods with gently rolling hills. Tributary streams are fairly well 

incised into the landscape, which occasionally opens into broad, forested floodplains. In the middle portion of the 

watershed, moderate to gently rolling hills with areas of prominent karstic features, such as sink depressions and 

captured streams, create surface relief. The lower watershed is primarily a broad, slightly undulating karst plain, 

with interspersed wetlands (FDEP 2001). 
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Figure 1.4 Santa Fe Planning Unit and major cities in study area. 

Table 1.3 WBIDs in the Santa Fe Planning Unit 

WBID Name 

3504 Olustee Creek 

3504A Olustee Creek 

3506 New River 

3506A New River 

3506B New River 

3513 Unnamed Slough 

3516 Alligator Lake Outlet 

3516A Alligator Lake 

3517 Price Creek 

3519 Ichetucknee River 

3519C Coffee Springs 

3519Q Mill Pond Spring 

WBID Name 

3519R Grassy Hole Spring 

3519S Mission Spring 

3519T Devil'S Eye Spring 

3519X Blue Hole Spring 

3519Y Cedar Head Spring 

3519Z Ichetucknee Head Sprin 

3520 Cannon Creek 

3522 Unnamed Slough 

3524 Turkey Creek 

3527 Unnamed Slough 

3530 Swift Creek 

3531 Rose Creek 

WBID Name 

3531A Rose Creek Sink 

3532 Grannybay Drain 

3535 Unnamed Branch 

3537 Unnamed Creek 

3539 Unnamed Slough 

3540 Unnamed Drain 

3541 Center Bay Drain 

3542 Unnamed Branch 

3545 Unnamed Slough 

3546 Richard Creek 

3547 Unnamed Branch 

3548 Unnamed Drain 
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WBID Name 

3549 Alligator Creek 

3552 Piney Bay Drain 

3553 Unnamed Drain 

3555 Unnamed Drain 

3557 Unnamed Slough 

3558 Unnamed Branch 

3559 Unnamed Branch 

3562 Unnamed Slough 

3563 Unnamed Branch 

3566 Lake Butler 

3566A Lake Butler Outlet 

3567 Wateroak Creek 

3570 Unnamed Slough 

3571 Cedar Hammock Drain 

3576 Unnamed Branch 

3578 Fivemile Creek 

3579 Gum Creek 

3583 Mckinney Branch 

3584 Unnamed Drain 

3585 Unnamed Branch 

3586 Fern Pond Drain 

3587 Browns Still Run 

3589 Unnamed Branch 

3590 Cypress Run 

3593 Lake Crosby Outlet 

3593A Lake Crosby 

3595 Unnamed Slough 

3596 Unnamed Branch 

3598 Sampson River 

3598B Lake Rowell 

3598C Alligator Creek 

3598D Lake Sampson 

3600 Hammock Branch 

3601 Unnamed Creek 

3602 Unnamed Branch 

3604 Unnamed Branch 

3605 Santa Fe River 

WBID Name 

3605A Santa Fe River 

3605B Santa Fe River 

3605C Santa Fe River 

3605D Santa Fe River 

3605E Santa Fe River 

3605F Altho Drainage 

3605G Santa Fe Lake 

3605H Lake Altho 

3605P Siphon Creek Rise (Gil 

3605Q Ala 112971 

3605R Santa Fe Rise 

3605S Devils Ear 

3605T Columbia Springs 

3605U Col 61981 (Spring) 

3605W Poe Spring 

3605X Blue Spring Gilchrist 

3605Y Ginnie Spring 

3605Z Trail Springs 

3606 Mined Area 

3609 Unnamed Branch 

3611 Unnamed Branch 

3612 Unnamed Creek 

3613 Unnamed Branch 

3614 Unnamed Slough 

3615 Unnamed Slough 

3616 Unnamed Ditch 

3617 Unnamed Branch 

3619 Unnamed Slough 

3620 Unnamed Branch 

3621 Unnamed Creek 

3622 Prevatt Creek 

3623 Unnamed Drain 

3625 Unnamed Creek 

3626 Pareners Branch 

3627 Unnamed Branch 

3629 Unnamed Slough 

3630 Double Run Creek 

WBID Name 

3632 Braggs Branch 

3633 Hampton Ditch 

3634 Unnamed Branch 

3635A Hampton Lake 

3635B Hampton Lake Outlet 

3637 Unnamed Branch 

3638 Unnamed Slough 

3639 Theressa Slough 

3641 Rocky Creek 

3642 Townsend Branch 

3644 Mill Creek Sink 

3646 Unnamed Slough 

3647 Unnamed Branch 

3648 Rhuda Branch 

3649 Cow Creek 

3649A Waters Lake 

3651 Unnamed Branch 

3653 Hornsby Spring Run 

3653Z Hornsby Spring 

3654 Monteocha Creek 

3655 Trout Pond Outlet 

3655A Trout Pond 

3656 Unnamed Drain 

3657 Unnamed Branch 

3658 Unnamed Creek 

3660 Unnamed Slough 

3663 Little Monteocha Creek 

3664 Unnamed Branch 

3665 Unnamed Drain 

3666 Unnamed Branch 

3667 Unnamed Drain 

3669 Unnamed Branch 

3670 Burnetts Lake Drain 

3671 Turkey Creek 

3678 Hague Branch 

3681 Turkey Creek 

3682 Blue Creek 

1.3 Background 

This report was developed as part of the Department’s watershed management approach for restoring and protecting 

state waters and addressing TMDL Program requirements. The watershed approach, which is implemented using a 

cyclical management process that rotates through the state’s 52 river basins over a 5-year cycle, provides a 

framework for implementing the TMDL Program–related requirements of the 1972 federal Clean Water Act and the 

1999 Florida Watershed Restoration Act (FWRA, Section 403.067, Florida Statutes [F.S.]) 

A TMDL represents the maximum amount of a given pollutant that a waterbody can assimilate and still meet water 

quality standards, including its applicable water quality criteria and its designated uses. TMDLs are developed for 
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waterbodies that are verified as not meeting their water quality standards, and provide important water quality 

restoration goals that will guide restoration activities. 

This TMDL report will be followed by the development and implementation of a Basin Management Action Plan, or 

BMAP, to reduce the amount of nutrients that caused the verified impairment of Suwannee River and Santa Fe 

River. These activities will depend heavily on the active participation of the SJRWMD, local governments, 

businesses, and other stakeholders. The Department will work with these organizations and individuals to undertake 

or continue reductions in the discharge of pollutants and achieve the established TMDLs for impaired waterbodies. 
TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River 

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Chapter 2: DESCRIPTION OF WATER QUALITY 

PROBLEM 

2.1 Statutory Requirements and Rulemaking History 

Section 303(d) of the Clean Water Act requires states to submit to the EPA a list of surface waters that do not meet 

applicable water quality standards (impaired waters) and establish a TMDL for each pollutant source in each of 

these impaired waters on a schedule. The Department has developed these lists, commonly referred to as 303(d) 

lists, since 1992. The list of impaired waters in each basin is also required by the FWRA (Subsection 403.067[4)] 

Florida Statutes [F.S.]), and the list is amended annually to include updates for each basin statewide. 

Florida’s 1998 303(d) list included 571 waterbodies in the Suwannee River Basin. However, the FWRA (Section 

403.067, F.S.) stated that all previous Florida 303(d) lists of impairments were for planning purposes only and 

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

waters. After a long rulemaking process, the Environmental Regulation Commission adopted the new methodology 

as Chapter 62-303, Florida Administrative Code (F.A.C.) (Identification of Impaired Surface Waters Rule, or IWR), 

in April 2001, and amended in 2006 and again in 2007. The list of waters for which impairments have been 

verified using the methodology in the IWR is referred to as the Verified List. 

Table 2.1 is the list of all waterbodies on the Cycle 2 verified list. This TMDL’s focus will be on nutrients and 

dissolved oxygen (DO) impairments. As required by the FWRA, the Verified List of impaired waters for the SRB 

and SFRB was adopted by Secretarial Order on June 3, 2008. Figures 2.1-2.3 show all the WBIDs located in the 

Middle Suwannee, Lower Suwannee, and Santa Fe Planning Units, respectively. 

Table 2.1 Cycle 2 Verified List for Suwannee River Basin 

Planning 

Unit 

WBID Water Segment Name 

Waterbody 

Type 

Water 

Class 

1998 

303(d) 

Parameter 

of Concern 

Parameters 

Assessed Using 

the IWR 

Priority for TMDL 

Development 

Lower 

Suwannee 3422 

Suwannee River 

(Lower) Stream 3F 

Nutrients (Hist 

Chlorophyll) High 

Lower 

Suwannee 3422D 

Lower Suwannee 

Estuary Estuary 3M 

Fecal Coliform 

(Shellfish) Low 

Lower 

Suwannee 3422D 

Lower Suwannee 

Estuary Estuary 3M 

Mercury (in 

fish tissue) High 

Lower 

Suwannee 3422R Manatee Springs Stream 3F 

Nutrients 

(Algal Mats) Medium 

Lower 

Suwannee 3422R Manatee Springs Stream 3F Iron Medium 

Lower 

Suwannee 3422S Fanning Springs Stream 3F 

Nutrients 

(Algal Mats) Medium 

Lower 

Suwannee 3422D 

Lower Suwannee 

Estuary Estuary 3M Chlorophyll High 

Lower 

Suwannee 3717 Unnamed Drain Estuary 3M 

Mercury (in 

fish tissue) High 

Lower 

Suwannee 3733 Direct Runoff To Gulf Stream 2 Fecal Coliform Low 

Lower 

Suwannee 3733 Direct Runoff To Gulf Stream 2 

Fecal Coliform 

(3) Low 
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Planning 

Unit 

WBID Water Segment Name 

Waterbody 

Type 

Water 

Class 

1998 

303(d) 

Parameter 

of Concern 

Parameters 

Assessed Using 

the IWR 

Priority for TMDL 

Development 

Middle 

Suwannee 3422B 

Suwannee River 

(Lower) Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3422J Branford Spring Stream 3F 

Nutrients 

(Algal Mats) Medium 

Middle 

Suwannee 3422J Branford Spring Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3422L Ruth Spring Stream 3F 

Nutrients 

(Algal Mats) Medium 

Middle 

Suwannee 3422P Mearson Spring Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3422Q Ellaville Spring Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3422T Troy Spring Stream 3F 

Nutrients 

(Algal Mats) Medium 

Middle 

Suwannee 3422T Troy Spring Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3422U Royal Spring Stream 3F 

Nutrients 

(Algal Mats) Medium 

Middle 

Suwannee 3422U Royal Spring Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3422V Convict Spring Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3422W Running Spring Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3422X Telford Spring Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3422Y Charles Spring Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3422Z Falmouth Spring Stream 3F 

Nutrients 

(Algal Mats) Medium 

Middle 

Suwannee 3422Z Falmouth Spring Stream 3F 

Mercury (in 

fish tissue) High 

Middle 

Suwannee 3496A Low Lake Lake 3F 

Dissolved 

Oxygen Medium 

Middle 

Suwannee 3480 Bethel Creek Stream 3F Fecal Coliform Low 

Middle 

Suwannee 3483 Peacock Slough Stream 3F 

Nutrients 

(Algal Mats) Medium 

Middle 

Suwannee 3528Z Lafayette Blue Springs Stream 3F 

Nutrients 

(Algal Mats) Medium 

Middle 

Suwannee 3528Z Lafayette Blue Springs Stream 3F 

Mercury (in 

fish tissue) High 

Santa Fe 

River 3506 New River Stream 3F Coliforms Fecal Coliform Low 

Santa Fe 

River 3520 Cannon Creek Stream 3F Fecal Coliform Medium 

Santa Fe 

River 3530 Swift Creek Stream 3F Turbidity Medium 

Santa Fe 

River 3626 Pareners Branch Stream 3F Fecal Coliform Medium 

Santa Fe 

River 3641 Rocky Creek Stream 3F BOD 5Day BOD Low 

Santa Fe 

River 3644 Mill Creek Sink Stream 3F 

Dissolved 

Oxygen Medium 
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Planning 

Unit 

WBID Water Segment Name 

Waterbody 

Type 

Water 

Class 

1998 

303(d) 

Parameter 

of Concern 

Parameters 

Assessed Using 

the IWR 

Priority for TMDL 

Development 

Santa Fe 

River 3644 Mill Creek Sink Stream 3F Fecal Coliform Low 

Santa Fe 

River 3649 Cow Creek Stream 3F Fecal Coliform Medium 

Santa Fe 

River 3681 Turkey Creek Stream 3F Fecal Coliform Medium 

Santa Fe 

River 3682 Blue Creek Stream 3F Fecal Coliform Low 

Santa Fe 

River 3504A Olustee Creek Stream 3F 

Dissolved 

Oxygen Medium 

Santa Fe 

River 3504A Olustee Creek Stream 3F Fecal Coliform Low 

Santa Fe 

River 3506A New River Stream 3F 

Dissolved 

Oxygen Medium 

Santa Fe 

River 3506A New River Stream 3F Fecal Coliform Low 

Santa Fe 

River 3516A Alligator Lake Lake 3F 

Dissolved 

Oxygen Medium 

Santa Fe 

River 3516A Alligator Lake Lake 3F Nutrients Nutrients (TSI) Low 

Santa Fe 

River 3519S Mission Spring Stream 3F 

Nutrients 

(Algal Mats) Medium 

Santa Fe 

River 3519T Devil'S Eye Spring Stream 3F 

Nutrients 

(Algal Mats) Medium 

Santa Fe 

River 3519X Blue Hole Spring Stream 3F 

Nutrients 

(Algal Mats) Medium 

Santa Fe 

River 3531A Rose Creek Sink Stream 3F 

Nutrients 

(Chlorophyll) Medium 

Santa Fe 

River 3531A Rose Creek Sink Stream 3F 

Dissolved 

Oxygen Medium 

Santa Fe 

River 3593A Lake Crosby Lake 3F 

Mercury (in 

fish tissue) High 

Santa Fe 

River 3598C Alligator Creek Stream 3F Fecal Coliform Low 

Santa Fe 

River 3598D Lake Sampson Lake 3F 

Mercury (in 

fish tissue) High 

Santa Fe 

River 3605A Santa Fe River Stream 3F 

Nutrients 

(Algal Mats) High 

Santa Fe 

River 3605C Santa Fe River Stream 3F 

Nutrients 

(Algal Mats) High 

Santa Fe 

River 3635A Hampton Lake Lake 3F 

Mercury (in 

fish tissue) High 

Santa Fe 

River 3605A Santa Fe River Stream 3F 

Dissolved 

Oxygen 

Dissolved 

Oxygen High 

Santa Fe 

River 3605C Santa Fe River Stream 3F 

Dissolved 

Oxygen 

Dissolved 

Oxygen High 

Santa Fe 

River 3605F Altho Drainage Stream 3F 

Dissolved 

Oxygen 

Dissolved 

Oxygen High 
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Figure 2.1 Middle Suwannee WBIDs 
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Figure 2.2 Lower Suwannee WBIDs 

.
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Figure 2.3 Santa Fe WBIDs 
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2.2 Information on Verified Impairment 

The Department used the IWR to assess water quality impairments in the main stems of the Suwannee and Santa Fe 

Rivers and verified that portions of the Suwannee and Santa Fe Rivers are impaired for dissolved oxygen (DO) and 

nutrients, based on data in the Department’s IWR database. 

2.2.1 Nutrients 

In this report nitrate is NO3 as nitrogen (NO3N) and for the purposes of this report, unless otherwise stated, the sum 

of NO3 and nitrite (NO2) is used to represent NO3 due to minimal contributions of NO2. Chapter 5 discusses the 

nitrate (NO3) nutrient impairment and the setting of the target concentration of NO3. 

Total Phosphorus (TP) rose in the SRB until it peaked in 1983 and has been generally declining since then (Figure 

2.4). The figure below was calculated by taking annual average phosphorus concentrations from all data collected 

within the main stems of the rivers for each planning unit and then calculating a three year rolling average to correct 

for annual climactic differences, such as rainfall. A significant decreasing trend (α=0.01) is observed when 

comparing the TP concentrations in the early 1980s to its present condition (Hornsby 2007). This trend was 

observed in all parts of the basin and does not track with records for mining activities. While mining activity has 

been present in the upper Suwannee since the 1960s, it does not appear to account for the trend below because the 

same trend is also observed in the Santa Fe River, which does have mining activity. The trend does track with 

fertilizer application (Figure 2.5 and Appendix C). The lag time between the two peaks can reasonably be explained 

by the time it takes for phosphorus to move through the soils and into the surrounding ground water and surface 

waters. 

The Department performed a regression analysis to determine if there was a correlation between phosphorus 

concentrations and flow. The maximum correlation coefficient found in all the regression for each planning unit 

was 0.42, leading us to conclude that flow was not a dominant factor effecting concentrations. 

Additionally, the Department could not find any climactic conditions that would generate this type of trend. A 

change point analysis was also conducted in the same manner as the nitrate in Chapter 5. This analysis is used to 

determine if there is a relationship between phosphorus concentrations and algal biomass or density. No relationship 

was observed for TP. In 2003, Quinlan found that the nitrogen was most widely the limiting nutrient in the estuary 

and that TP was rarely the limiting nutrient. For the purposes of this TMDL the Department could not link the 

impairments with either phosphorus load or concentration and, therefore, will be targeting NO3 to achieve standards. 

Monitoring and evaluation for total phosphorus should continue as this TMDL is implemented. 
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Figure 2.4 Total Phosphorus-Three Year Rolling Average by Planning Unit 

TP MOVING 3 YEAR AVERAGE

0.000

0.100

0.200

0.300

0.400

0.500

1965 1970 1975 1980 1985 1990 1995 2000 2005 2010

YEAR

TOTAL PHOSPHORUS 

(MG/L)

LOWER SANTA FE LOWER SUWANNEE MIDDLE SUWANNEE

Figure 2.5 Rolling Average TP concentrations for the Middle Suwannee River and TP fertilizer sales for 

Suwannee and Lafayette counties 

Long Term TP Fertilizer Sales

0

1000

2000

3000

4000

5000

6000

1945 1953 1961 1969 1977 1985 1992 2000

Year

TP (Tons)

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

TP (mg/L)

TP (Tons)

Rollinng average TP
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2.2.2 Dissolved Oxygen 

Tables 2.2 through 2.4 summarize the DO data for the verification period, which for Group 1 waters was June 1, 

2000, through June 30, 2007, by month, season, and year, respectively. There is a 35 % overall exceedance rate for 

DO in Suwannee and Santa Rivers during the verified period. During the verified period, samples ranged from 0.9 

to 11.93 milligrams per liter (mg/L). 

When aggregating data by season, the lowest percentage of exceedances occurred in the winter and the highest in 

spring/summer. Possible relationships between DO and other water quality parameters will be further assessed 

using the complete historical dataset in Chapter 5. 

Table 2.2 Summary of DO Data by Month for the Verified Period (June 1, 2000 – June 30, 2007) 

WBID Month 

Number of 

Observations 

DO 

Min 

DO 

Max 

DO 

Mean 

DO 

Median 

Number of 

Exceedances Exceedance Rate 

1 8 5.4 7.4 6.08 5.9 0 0.00% 

2 8 5.5 7.1 6.18 6.0 0 0.00% 

3 11 3 7 5.92 6.1 2 18.18% 

4 8 2.6 7 5.60 6.2 2 25.00% 

5 8 4.3 8.2 6.19 6.35 2 25.00% 

6 9 4.5 6.9 5.99 6.2 1 11.11% 

7 12 4 8.86 6.72 6.8 2 16.67% 

8 7 4.7 6.2 5.50 5.7 2 28.57% 

9 16 4.3 6.74 5.60 5.7 1 6.25% 

10 7 1.8 5.69 4.87 5.3 1 14.29% 

11 7 3.6 6.22 5.63 5.9 1 14.29% 

12 12 5 8.41 6.63 6.6 0 0.00% 

3605A 

1 39 3.14 9.6 5.99 5.8 10 25.64% 

2 45 3.9 10.19 5.86 5.3 16 35.56% 

3 48 3.3 11.93 5.45 5.1 20 41.67% 

4 48 2.5 9.9 4.67 4.7 33 68.75% 

5 45 1.8 7.7 5.00 5.05 18 40.00% 

6 49 2.4 9.3 5.10 4.7 27 55.10% 

7 38 2.4 9.9 5.08 4.95 19 50.00% 

8 43 1.2 5.99 3.87 4.2 35 81.40% 

9 87 1.02 6.11 3.47 3.7 84 96.55% 

10 41 0.9 9.1 3.36 3.7 39 95.12% 

11 41 2.04 6.2 4.04 4.5 31 75.61% 

12 41 1.1 8.5 5.04 5.1 19 46.34% 

3605C 

Table 2.3 Summary of DO Data by Season for the Verified Period (June 1, 2000 – June 30, 2007) 

WBID Month 

Number of 

Observations 

DO 

Min 

DO 

Max 

DO 

Mean 

DO 

Median 

Number of 

Exceedances Exceedance Rate 

WINTER 27 3 7.4 6.04 6.1 2 7.41% 

SPRING 25 2.6 8.2 5.93 6.2 5 20.00% 

SUMMER 35 4 8.86 5.97 5.8 5 14.29% 

FALL 26 1.8 8.41 5.89 6 2 7.69% 

3605A 
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WBID Month 

Number of 

Observations 

DO 

Min 

DO 

Max 

DO 

Mean 

DO 

Median 

Number of 

Exceedances Exceedance Rate 

WINTER 132 3.14 11.93 5.75 5.3 46 34.85% 

SPRING 142 1.8 9.9 4.92 4.8 78 54.93% 

SUMMER 168 1.02 9.9 3.94 4 138 82.14% 

FALL 123 0.9 9.1 4.15 4.1 89 72.36% 

3605C 

Table 2.4 Summary of DO Data by Year for the Verified Period (June 1, 2000 – June 30, 2007) 

WBID Month 

Number of 

Observations 

DO 

Min 

DO 

Max 

DO 

Mean 

DO 

Median 

Number of 

Exceedances Exceedance Rate 

1999 14 5.3 6.5 6.04 6.15 0 0.00% 

2000 18 5.1 8.2 6.46 6.5 0 0.00% 

2001 15 5 8.1 6.05 5.9 0 0.00% 

2002 17 5.3 8.86 6.59 6.2 0 0.00% 

2003 16 2.6 7.8 5.01 5.15 8 50.00% 

2004 12 1.8 6.6 5.43 6.05 2 16.67% 

2005 15 3.8 8.41 5.81 5.8 4 26.67% 

2006 6 5.9 6.5 6.18 6.2 0 0.00% 

3605A 

1999 63 1.5 6.7 4.28 4.7 40 63.49% 

2000 62 1.2 7.7 4.49 4.5 33 53.23% 

2001 71 1.02 11.93 4.94 4.6 37 52.11% 

2002 66 0.9 9.9 4.96 4.7 40 60.61% 

2003 113 1.8 9.1 4.28 4.3 84 74.34% 

2004 82 1.6 9.6 4.70 4.7 53 64.63% 

2005 71 2.57 7.6 4.54 4.49 49 69.01% 

2006 37 3.1 9.6 5.76 5 15 40.54% 

3605C 
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2.2.3 Sampling Sites 

Figures 2.6-2.8 show the locations of the data collection sampling sites. 

Figure 2.6 Middle Suwannee Aerial and Sampling Station Locations 
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Figure 2.7 Lower Suwannee Aerial and Sampling Station Locations 
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Figure 2.8 Santa Fe Aerial and Sampling Station Locations 
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The Suwannee River Water Quality Report 2000 documents the effect of nitrate on the Suwannee River. The 

reports states there are “significant positive relationships between nitrate and total periphyton biomass and algal 

density, meaning that higher nitrate levels appear to result in increased algal abundance.” In the years prior to the 

report there were flow events that led to extensive growth of filamentous algae in the Suwannee and Santa Fe 

Rivers. Figure 2.9 provides photographic documentation of the blooms (Hornsby et al, 2000). Excessive algal 

growth is also documented by the photographic evidence shown in Figure 2.10. 

Figure 2.9 Photographic evidence 2000 
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Figure 2.10 Additional Photographic Evidence. 
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Chapter 3: DESCRIPTION OF APPLICABLE WATER 

QUALITY STANDARDS 

3.1 Classification of the Waterbody and Criteria Applicable to the TMDL 

Florida’s surface waters are protected for five designated use classifications, as follows: 

Class I Potable water supplies 

Class II Shellfish propagation or harvesting 

Class III Recreation, propagation, and maintenance of a healthy, well-balanced population of fish and 

wildlife 

Class IV Agricultural water supplies 

Class V Navigation, utility, and industrial use (there are no state waters currently in this class) 

Both the Suwannee River and Santa Fe River are Class III waterbodies, with a designated use of recreation, 

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

quality criteria applicable to the impairment addressed by this TMDL are for nutrients and dissolved oxygen. 

3.2 Interpretation of Dissolved Oxygen Criterion and Narrative Nutrient 

The following is the relevant sections Rule 62-302 F.A.C for fresh and marine waters. 

Dissolved Oxygen Criterion 

62-302.530 Table: Surface Water Quality Criteria 

Criteria for Surface Water Quality Classifications 

 Class III: Recreation, Propagation and Maintenance of a Healthy, Well-Balanced 

Population of Fish and Wildlife 

Parameter Units 

Predominantly Fresh Waters Predominantly Marine Waters 

(30) Dissolved 

Oxygen 

Milligrams/L Shall not be less than 5.0. Normal 

daily and seasonal fluctuations above 

these levels shall be maintained. 

Shall not average less than 5.0 in a 24-hour 

period and shall never be less than 4.0. 

Normal daily and seasonal fluctuations above 

these levels shall be maintained. 

The nutrient criterion in Rule 62-302, F.A.C., is expressed as a narrative: 

Nutrients: 

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 [Note: For Class III waters in the Everglades Protection Area, this criterion has 

been numerically interpreted for phosphorus in Section 62-302.540, F.A.C.]. 

Florida’s nutrient criterion is narrative only—i.e., nutrient concentrations of a body of water shall not be altered so 

as to cause an imbalance in natural populations of aquatic flora or fauna. Accordingly, a nutrient-related target was 

needed to represent levels above which an imbalance in flora or fauna is expected to occur. A threshold commonly 

used for assessing the nutrient impairment in streams is the annual average chl a concentration of 20 μg/L, which is 

defined in the Impaired Waters Rule (IWR, 62-303 F.A.C). In addition, the IWR also allows the use of other 

information indicating imbalance in flora or fauna due to nutrient enrichment, including, but not limited to, algal 

blooms, excessive macrophyte growth, decrease in the distribution (either in density or areal coverage) of seagrasses 

or other submerged aquatic vegetation, changes in algal species richness, and excessive diel oxygen swings. 
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3.3 Outstanding Florida Waters Classification (OFW) 

Section 403.061(27), Florida Statutes, grants DEP the power to: Establish rules which provide for a special category 

of waterbodies within the state, to be referred to as “Outstanding Florida Waters,” which shall be worthy of special 

protection because of their natural attributes. Most OFWs are areas managed by the state or federal government as 

parks, wildlife refuges, preserves, marine sanctuaries, estuarine research reserves, certain waters within state or 

national forests, scenic and wild rivers, or aquatic preserves. The Suwannee River and Santa Fe Rivers are both 

designated “Special Waters” because of their exceptional ecological and recreational significance. 

The Suwannee River was designated an OFW in 1979. That year (pre-OFW) the annual NO3-N load was 3,548,981 

kg N yr-1 and in 2005(post-OFW) the annual NO3-N load was 6,197,855 kg N yr-1 (Hornsby, 2007). The Santa Fe 

River was designated an OFW in 1984. 

3.4 Watershed Management Basin Rotation Cycle 1 

The Watershed Management Program is responsible for fostering better stewardship of Florida’s ground and surface 

water resources. Working with other state agencies, water management districts, local governments, citizens, and 

the private sector, the bureau coordinates the collection, data management, and interpretation of monitoring 

information to assess the health of our water resources; develops watershed-based aquatic resource goals and 

pollutant loading limits for individual waterbodies; and develops and implements management action plans to 

preserve or restore waterbodies. These activities are undertaken using the rotating basin approach that assures that 

the watershed plans for each of the state’s watersheds are evaluated and updated every five years. 

In the first cycle rotation the Santa Fe River was verified for impairments of Nutrients (WBID 3605A) due to algal 

mats and historical chlorophyll and dissolved oxygen (WBID3605B) linked to nutrients. 

3.5 Suwannee River Partnership and Reasonable Assurance Documentation 

During the first Suwannee Basin assessment under the Watershed Management Program in 2002, portions of the 

Suwannee and Santa Fe Rivers impairments were identified for dissolved oxygen and nutrients. The listing process 

included an option to not place waters on the adopted verified list if Reasonable Assurance (RA) could be 

demonstrated by responsible entities that a management plan was in place that would restore water quality to 

achieve its designated use and a TMDL was not necessary. 

The Suwannee River Partnership, a coalition of state, federal and regional agencies, local governments and private 

industry representatives that had been formed in 1999 to reduce nitrate levels in the surface and ground water of the 

Middle Suwannee watershed submitted a RA document to the Department in 2002. 

On June 11, 2003, in the EPA’s decision document, the EPA while recognizing “that the efforts of the partnership 

have realized great success in gaining commitments in the Middle Suwannee that should result in water quality 

improvements once executed” did not accept the Partnership’s RA documentation. The EPA sited that “similar 

commitments have not been initiated in the Upper Suwannee and Santa Fe watersheds. Attaining water quality 

standards in the Suwannee basin, including the estuary, will require that control strategies be in place in the Upper 

Suwannee and Santa Fe watersheds as well as the Middle Suwannee.” Since then, the Partnership expanded its work 

to include the Santa Fe River Basin and the entire Suwannee River Water Management District area. 
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Chapter 4: ASSESSMENT OF SOURCES 

4.1 Types of Sources 

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

individual sources of the pollutant of concern in the target 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 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 on the federal and state 

stormwater programs). 

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

sources (such as domestic and industrial wastewater discharges) AND stormwater systems requiring an NPDES 

stormwater permit when allocating pollutant load reductions required by a TMDL (see Section 6.1 on Expression 

and Allocation of the TMDL). However, the methodologies used to estimate nonpoint source loads do not 

distinguish between NPDES and non-NPDES stormwater discharges, and as such, this source assessment section 

does not make any distinction between the two types of stormwater. 

4.2 Point Sources in the Suwannee River Basin 

Table 4.1 and Figures 4.1-4.4 identify the facilities authorized as permitted discharges in the Suwannee River Basin. 

As the seven NPDES point sources are either outside the watersheds of interest (they do not discharge into the 

impaired waters covered by this TMDL) or do not have a direct effect on the nutrient levels in the Middle or Lower 

Suwannee River or Santa Fe River Basins, no WLAs are assigned. 

Table 4.1 Permitted facilities identified in the drainage basin discharge to Suwannee River Basin 

FACILITY 

ID 

FACILITY NAME Facility Type 

DESIGN 

Capacity 

(MGD) COUNTY 

FL0000051 

EI Dupont De Nemours 

Trailridge Mine IW 30.0 Bradford 

FL0000183 

Progress Energy FL - 

Suwannee River Power 

Plant 

IW 

342.0 Suwannee 

FL0001465 

Pilgrim's Pride Processing 

Plant 

IW 

1.5 Suwannee 

FL0028126 Starke, City of WWTF DW 1.65 Bradford 

FL0038300 Mead Westvaco Corp IW 0.0482 Columbia 

FL0043567 Cochran Forest Products IW 0.05 Columbia 

FL0189120 

High Springs Commercial 

Park WWTF DW 0.03 Alachua 

FLA011323 IFAS - Dairy Research CFO 0.151 Alachua 
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FACILITY 

ID 

FACILITY NAME Facility Type 

DESIGN 

Capacity 

(MGD) COUNTY 

Unit 

FLA116173 

Dairy Production Systems 

- Branford Farm CFO 0.175 Gilchrist 

FLA116190 Piedmont Dairy CFO 0.045 Gilchrist 

FLA116521 Alliance Dairies CFO 0.37 Levy 

FLA161977 Oak Grove Dairy, Inc CFO 0.11 Dixie 

FLA184047 Lafayette Dairy CFO Lafayette 

FLA184993 Hill Top Dairy CFO Gilchrist 

FLA282821 North Florida Holsteins CFO Gilchrist 

FLA285331 

Bell Farm (FKA Aurora 

1) CFO Gilchrist 

FLA362778 Shenandoah Dairy CFO Suwannee 

FLA371912 Full Circle Dairy, LLC CFO Madison 

FLA470031 Suwannee Farms Inc CFO Suwannee 

FLG110015 

A Materials Group Inc - 

Plant #11 CBP Columbia 

FLG110073 

Florida Rock Industries 

Inc - High Springs CBP CBP Alachua 

FLG110190 

Florida Rock Industries - 

Starke CBP CBP Bradford 

FLG110278 Bell Concrete Products CBP Gilchrist 

FLG110304 

Columbia Ready Mix 

Concrete Inc 

CBP 

 Columbia 

FLG110369 

A Materials Group Inc - 

Plant #12 

CBP 

 Levy 

FLG110370 Bell Concrete CBP Levy 

FLG110374 

Columbia Ready Mix 

Concrete Inc 

CBP 

 Suwannee 

FLG110450 

Mayo Ready Mix 

Concrete 

CBP 

 Lafayette 

FLG110558 

Mayo Ready Mix 

Concrete 

CBP 

 Lafayette 

FLG911679 

Badcock Live Oak 

Warehouse PET Suwannee 

FLS000062 

Lake City, City of - 

WWTF WWTP ISW Columbia 

FLS000062 

Lake City, City of - 

WWTF WWTP ISW Columbia 

IW Industrial Wastewater 

DW Domestic 

CFO Concentrated Animal Feeding Operation 

CBP Concrete Batch 

PET Petroleum Cleanup GP (long term) 

WWTP ISW Individual Stormwater 
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Figure 4.1 Wastewater Facilities in the Middle Suwannee River Basin. 
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Figure 4.2 Wastewater Facilities in the Lower Suwannee River Basin. 
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Figure 4.3 Wastewater Facilities in the Santa Fe River Basin. 
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4.2.1 Municipal Separate Storm Sewer System Permittees 

A municipal separate storm sewer system (MS4) is a publicly-owned conveyance or system of conveyances (i.e., 

ditches, curbs, catch basins, underground pipes, etc.) that is designed or used for collecting or conveying stormwater 

and that discharges to surface waters of the State. Table 4.2 show the Phase II MS4 permits in the Santa Fe River 

Basin. The Department welcomes input from the MS4 permittees regarding the extent of their discharges in the 

WBIDs of concern. There are no MS4 Permittees in the Middle and Lower Suwannee River Planning Units. 

Table 4.2 MS4 Permittees 

County Permitee 

Permit 

Number Phase 

Alachua University of Florida FLR04E067 Phase II 

Alachua FDOT District 2 (Gainesville UA) FLR04E018 Phase II 

Alachua Alachua County FLR04E005 Phase II 

Alachua City of Gainesville FLR04E006 Phase II 

4.3 Nonpoint Sources 

Potential nonpoint sources of total nitrogen in the watershed were calculated in Figures 4.4-4.6 using the equations 

in Hornsby 1997 and data from 2007. Estimates of total nitrogen for humans, poultry, beef, and dairy are based on 

the percentage of total nitrogen in raw waste and population size. 

Figure 4.4 Total Nitrogen inputs in the Middle Suwannee 

Middle Suwannee

Beef

9.1%

Fertilizer

40.8%

Dairy

14.7%

Human

2.0%

Poultry

21.7%

Atmospheric

11.7%

Total Nitrogen

66,005,375 lbs
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Figure 4.5 Total Nitrogen inputs in the Lower Suwannee 

Figure 4.6 Total Nitrogen inputs in the Santa Fe 

Santa Fe

Beef

14.6%

Fertilizer

48.0%

Dairy

12.2%

Human

9.3%

Poultry

2.3%

Atmospheric

18%

Total Nitrogen

41,944,865 lbs

Lower Suwannee

Beef

12.6%

Fertilizer

49.3%

Dairy

17.0%

Human

2.9%

Poultry

0.4%

Atmospheric

18%

Total Nitrogen

24,381,502 lbs
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4.3.1 Onsite Sewage Treatment and Disposal Systems 

In 1993 a report on onsite sewage treatment and disposal systems (OSTDS) found that over two-thirds of septic 

systems in the ten year floodplain of the Suwannee River were not functioning properly, installed incorrectly or in 

need of repair (HRS 1993). Figure 4.4 and Table 4.3 depict the number and location of OSTDS in the SRB. The 

Department at this time has only an estimated number of OSTDS in the SRB (DOH, 2007). 

Table 4.3 Estimated Number of Onsite Sewage Treatment Systems 

Planning Unit Number of Sites* 

Middle Suwannee 4,894 

Lower Suwannee 4,630 

Santa Fe 11,684 

*Number of onsite sewage treatment and disposal system sites is estimated from Department of Health information and does not constitute the 

actual number of onsite sewage treatment systems in the area. 

Figure 4.7 Onsite Sewage in the Suwannee River Basin 
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4.3.2 Human Population 

Table 4.4 and Figures 4.5-4.7 depict the populations in the individual planning units and their population densities 

(people per acre). 

Table 4.4 Population and number of household in SRB 

Middle 

Suwannee 

Total 

households 

1-person 

household 

2-person 

household 

3-person 

household 

4-person 

household 

5-person 

household 

6-person 

household 

7-or-more 

person 

household 

Total 12503 3035 4567 2045 1670 745 265 176 

Fraction of Total 1.00 0.23 0.41 0.18 0.14 0.05 0.00 0.00 

% of Total 100 22.73 40.91 18.18 13.64 4.55 0.00 0.00 

# of People 31532 3035 9135 6136 6679 3723 1592 1232 

Average Household 

Size 2.52 

Lower 

Suwannee 

Total 

households 

1-person 

household 

2-person 

household 

3-person 

household 

4-person 

household 

5-person 

household 

6-person 

household 

7-or-more 

person 

household 

Total 9053 2200 3590 1411 1091 491 163 106 

Fraction of Total 1.00 0.24 0.40 0.16 0.12 0.05 0.02 0.01 

% of Total 100 24.30 39.65 15.58 12.05 5.43 1.80 1.18 

# of People 22158 2200 7180 4232 4364 2456 980 745 

Average Household 

Size 2.45 

Santa Fe 

Total 

households 

1-person 

household 

2-person 

household 

3-person 

household 

4-person 

household 

5-person 

household 

6-person 

household 

7-or-more 

person 

household 

Total 33348 7558 11979 5918 4759 2005 714 416 

Fraction of Total 1.00 0.23 0.36 0.18 0.14 0.06 0.02 0.01 

% of Total 100 22.66 35.92 17.75 14.27 6.01 2.14 1.25 

# of People 85523 7558 23958 17755 19034 10023 4281 2914 

Average Household 

Size 2.56 
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Figure 4.8 Middle Suwannee Basin Population Density 
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Figure 4.9 Lower Suwannee Basin Population Density 
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Figure 4.10 Santa Fe Basin Population Density. 
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4.3.3 Animal Operations 

Table 4.5 shows the estimated population sizes of animal operations in the SRB. Table 4.6 provides the estimates of 

the annual contribution of total nitrogen by human and animal operations (USDA 2007). Using the annual 

contribution numbers, an estimated equivalent human population of approximately 3,800,000 in the SRB was 

calculated based on the amount of nitrogen contributed annually. 

Table 4.5 Animal Operations 2007 Estimates by planning unit 

Population 

Planning Unit Human (Census 2007) 

Middle 66,749 

Lower 70,905 

Santa Fe 354,268 

Beef Cattle 

Middle 30,000 

Lower 31,000 

Santa Fe 47,500 

Milk Cows and calf 

Middle 21,000 

Lower 18,000 

Santa Fe 4,200 

Poultry 

Middle 49,965,391 

Lower 79,006 

Santa Fe 6,465,663 

Table 4.6 Total Nitrogen contribution estimates. 

 

Population 

Total 

Annual TN 

contribution (Tons) Conversion* Mean wt

Human 491,922 2,424 0.2 lbs. N/1000 lbs. / day 135 lbs. 

Milk Cows 58,900 6,772 0.45 lbs. N/1000 lbs. / day 1400 lbs. 

Beef Cattle 116,500 5,783 0.34 lbs. N/1000 lbs. / day 800 lbs. 

Poultry 56,510,060 4,050 1.10 lbs. N/1000 lbs. / day ** 2 lbs. 

Estimated 

Equivalent 

Human 

population 3,861,899 

* ASTM Standard Conversion 

** Calculated for 6 flocks for 6 weeks or chicken on ground 252 

days/year; weight averaged over life 

4.3.4 Agriculture 

In 2004 Agriculture amounted to the second largest land use and was approximately 24% of all land use. Table 4.7 

show the estimated areas of agriculture uses in the SRB from 2004 land use data. 

Middle Suwannee Lower Suwannee Santa Fe 

Agriculture Land Use Acres Percent Acres Percent Acres Percent 

Improved Pastures 52,234 32 41,126 43 88,583 49 

Hay Fields 40,127 25 17,882 19 6,965 4 

Field Crops 21,627 13 16,711 17 36,985 20 

Woodland Pastures 15,413 10 7,687 8 17,161 9 

Unimproved Pastures 14188 9 5296 6 20166 11 

Row Crops 7964 5 3610 4 6215 3 
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4.3.5 Land Uses 

Table 4.7 shows the changes in land use and the different percentages of use from 1988 to 2004. Differences in acres 

and total acre can be attributed to different methods of measurement and quantification of land use. In 2004 the 

largest percentage of land use was upland forests, approximately 30% of which was silviculture, followed by 

agriculture. Figures 4.4-4.12 show the current land use, population density and the changes over time. 

Table 4.7 Acreages and percent acreages of different land use categories for the SRB. 

Middle Suwannee 

1988 1995 2004 

Acres Percent Acres Percent Acres Percent 

Urban and Built Up 7,078 1.1 46,041 7.5 39,305 6.4 

Agriculture 207,477 33.6 178,715 29.0 162,035 26.3 

Rangeland 162048 26.3 5,969 1.0 17,338 2.8 

Upland Forest 179,827 29.2 318,181 51.6 309,527 50.2 

Water 5,170 0.8 5,335 0.9 4,485 0.7 

Wetland 51,766 8.4 57,618 9.3 77,070 12.5 

Barren Land 2,745 0.4 87 0.0 1,768 0.3 

Transportation, 

Communication & Utilities 684 0.1 4,849 0.8 5,268 0.9 

Total 616,795 616,795 616,795 

Lower Suwannee 

1988 1995 2004 

Acres Percent Acres Percent Acres Percent 

Urban and Built up 2,561 0.7 46,171 11.8 32,789 8.3 

Agriculture 121,908 31 103175 26.3 96,146 24.4 

Rangeland 56,239 14 4,989 1.3 10,226 2.6 

Upland Forest 130,088 33 161,004 41.0 172,734 43.8 

Water 8,322 2 7,056 1.8 7,948 2.0 

Wetland 68,088 17 68,490 17.4 72,266 18.3 

Barren Land 4,753 1 48 0.0 894 0.2 

Transportation, 

Communication & Utilities 457 0.1 1,574 0.4 1,688 0.4 

Total 392,416 392,506 394,692 

Santa Fe 

1988 1995 2004 

Acres Percent Acres Percent Acres Percent 

Urban and Built up 20,434 2.3 80,157 8.8 102,838 12 

Agriculture 182,780 20.2 198,045 21.7 182,758 21 

Rangeland 192,834 21.3 12,505 1.4 26,507 3 

Upland Forest 364,852 40.3 458,294 50.1 399,180 45 

Water 14,283 1.6 15,652 1.7 14,002 2 

Wetland 123,716 13.7 140,363 15.3 149,684 17 

Barren Land 3,643 0.4 441 0.05 2,064 0.2 

Transportation, 

Communication & Utilities 1,766 0.2 9,155 1.0 8,757 1.0 

Total 904,308 914,611 885,791 
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Figure 4.11 Principal land uses in the drainage basin of the Middle Suwannee River. 

 
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Figure 4.12 Principal land uses in the drainage basin of the Middle Suwannee River. 

Land Use Middle Suwannee

0

50000

100000

150000

200000

250000

300000

350000

400000

450000

500000

Urban and Built up 

Agriculture

Rangeland

Upland Forest

Water

Wetland

Barren Land

Transportation,

Communication &

Utilities

Acres

1988

1995

2004

 
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Figure 4.13 Principal land uses in the drainage basin of the Lower Suwannee River. 
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Figure 4.14 Principal land uses in the drainage basin of the Lower Suwannee River.

Lower Suwannee Land Use

0

20000

40000

60000

80000

100000

120000

140000

160000

180000

200000

Urban and Built up 

Agriculture

Rangeland

Upland Forest

Water

Wetland

Barren Land

Transportation,

Communication &

Utilities

Acres

1988

1995

2004
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Figure 4.15 Principal land uses in the drainage basin of the Santa Fe River. 
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Figure 4.16 Principal land uses in the drainage basin of the Santa Fe River 

Santa Fe Land Use

0

50000

100000

150000

200000

250000

300000

350000

400000

450000

500000

Urban and Built up 

Agriculture

Rangeland

Upland Forest

Water

Wetland

Barren Land

Transportation,

Communication &

Utilities

Acres

1988

1995

2004
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Chapter 5: DETERMINATION OF ASSIMILATIVE 

CAPACITY 

Often the Department will use a hydraulic and water quality model to simulate loading and the effect of the loading 

within a given waterbody. However, there are other appropriate methods to develop a TMDL that are just as 

credible as a modeling approach. Such an alternative approach was used to estimate existing conditions and 

calculate a TMDL. 

5.1 Hydrology 

A study by the USGS in cooperation with the SRWMD in 1999 found that the porous karst topography of the region 

has facilitated increased nitrate concentrations in the ground water inflow to the river stemming from increases in 

anthropogenic activities. “Agricultural activities (cropland farming, animal farming operations (beef and dairy 

cattle, poultry, and swine), along with atmospheric deposition, have contributed large quantities of nitrogen to 

ground water in the Suwannee River Basin in northern Florida” (Katz et al, 1999). 

In the SRB, the Floridian aquifer is both confined and unconfined (Figure 5.1). A layer of clay and then limestone 

over the confined portion of the aquifer decrease the contribution of rainwater and runoff to the aquifer. In contrast, 

the unconfined is capable of being recharged directly by rainfall and runoff allowing water soluble contaminants, 

such as nitrate, to enter the aquifer rapidly. 
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Figure 5.1 Floridian Aquifer 
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5.2 Water Quality Over Time 

The pre-OFW and post-OFW data were analyzed in a report prepared for the Department in 1999 by Janicki 

Environmental. The analyses suggested that there has been a statistically significant increase in NO3 concentrations 

and loadings since the OFW designation of the Suwannee River in 1979. 

On the Suwannee River, the area where the largest increase in nitrate concentration occurs is a 38 mile segment of 

the Middle Suwannee River Basin from Dowling Park to Branford. In the Santa Fe River the largest increase is 

from US 441 to State Road 47 (Hornsby 2007). The monitoring site at Branford has a data record for nitrates from 

1954 to 2007 (Figure 5.2) and shows an increasing trend in nitrate. The Santa Fe River’s lower three WBIDs 

(3605A, 3605B, 3605C) were combined to show the historic trends in NO3 (Figure 5.3). 

Figure 5.2 Historic Nitrate Data for the Suwannee River at Branford, FL 

Historic Nitrate Data for Suwannee River at Branford, FL

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

1954 1959 1967 1972 1977 1982 1989 1994 1999 2004

Year

NO3 (mg/L)

Rolling Average Nitrate

OFW 

Designation
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Figure 5.3 Historic Nitrate Data for the Santa Fe River 

Historic Nitrate Data for Santa Fe River

0

0.1

0.2

0.3

0.4

0.5

0.6

1959 1964 1969 1974 1979 1984 1989 1994 1999 2004

Year

NO3 (mg/L)

Rolling Average Nitrate

OFW

Designation
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5.3 Flows over time 

The USGS has flow record at the Branford site from 1931 to 2007. Figure 5.4 shows that the flow has not changed 

significantly when comparing the cumulative frequency profile for first forty years of the record to the present 36 

year record (Figure 5.3) 

Figure 5.4 Historic Flow Data Branford FL 

Branford Histroic Flow Data

0.00%

20.00%

40.00%

60.00%

80.00%

100.00%

0 5000 10000 15000 20000 25000 30000 35000 40000 45000 50000

Flow(cfs)

Quantiles

1931-1971

1972-2007
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Flows have not changed significantly, but loads of nitrate in the OFW baseline (3,548,981 kg N yr-1 in 1979) 

climbed significantly, to as high as 6,197,655 kg N yr-1 in 2005 (Figure 5.3). This indicates that the increasing trend 

of nitrate in the SRB has cumulated in an approximately 75% increase in loading to the Gulf of Mexico (Hornsby, 

2007) 

Figure 5.5 Nitrates Loads from the Suwannee River to the Gulf of Mexico from 1998-2005 (Hornsby 2007) 

Nitrate Load and Discharge over time

0

1,000,000

2,000,000

3,000,000

4,000,000

5,000,000

6,000,000

7,000,000

1998 1999 2000 2001 2002 2003 2004 2005

Year

Nitrate Load (kg N/yr)

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

18,000

Mean Discharge (cfs)

Nitrate Load (kg N/year)

Mean Discharge (cfs)

OFW Baseline

5.4 Biological Effects 

In 2003, Quinlan found that nutrient loads into the Suwannee River estuary were followed by increased patterns in 

annual mean algal biomass. “During higher freshwater discharge the nutrient-rich plume extended seaward and 

phytoplankton biomass increased because of increased nutrient availability.” This same study also found that the 

most widely limiting nutrient was nitrogen. 

5.5 Nitrate (NO3) Target 

The target nitrate concentration for the Suwannee and Santa Fe River Basins was established based on several lines 

of evidence, including 1) laboratory nutrient amendment bioassays, 2) comparing metabolic rates, specifically, 

ecological efficiency, of aquatic communities, 3) examining the ecological condition of algae and nutrients in 

Florida Springs Report, and 4) examining the relationship between periphyton biomass and cell density and the 

nitrate concentration in SRB and SFRB. 

5.5.1 Laboratory nutrient amendment bioassays 

The nutrient amendment bioassay work was conducted by Cowell and Dawes (2004), who examined the required 

nitrate concentration in the Rainbow River, Marion County, Florida to achieve a reduction of biomass of Lyngbya 

wollei. L. wollei is a nuisance blue-green benthic algal species that dominates the Rainbow River due to elevated 
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nitrate concentrations. Using Lyngbya cultures incubated in a series of nitrate amendments, Cowell and Dawes 

(2004) found that, at the end of the nutrient amendment experiments, both the biomasses and growth rates were low 

in treatment groups, with nitrate concentration at or below 300 μg/L, while the growth rates and biomass were 

significantly higher in treatments with nitrate concentrations at or higher than 600 μg/L. In addition, the experiment 

also showed that the biomass and growth rate in 300 and 70 μg/L treatment groups were similar, suggesting that 

further reduction of nitrate concentration below the 300 μg/L level probably would not achieve dramatic further 

reduction of L. wollei. A nitrate concentration of 300 μg/L should be appropriate in controlling L. wollei. 

5.5.2 Relationship between ecological efficiency and nitrate concentration 

Wetland Solutions, Inc (WSI, 2005) studied the effects of nutrient concentrations on the community metabolic rates 

in the Wekiva River (WR), Rock Springs Run (RSR), Alexander Springs Creek (ASC) and Juniper Creek (JC). The 

gross community primary production, community respiration, net primary production, and ecological efficiency 

were measured and examined. The community metabolic parameter shown to have a significant functional 

relationship with nutrient concentrations was ecological efficiency, which is defined as the quotient between the rate 

of gross primary productivity (GPP) and the incident photosynthetically active radiation (PAR) during a specified 

time interval. It is an ecosystem-level property that estimates the overall efficiency of an aquatic ecosystem to 

utilize incident solar radiation. Figure 5.6 shows the correlation between the ecological efficiency and nitrate 

concentration. 

Figure 5.6 Correlation between ecological efficiency and nitrate concentration in WR, RSR, ASC, and JC. 

The target ecological efficiency defined using this method is 0.25 g O2/mol. Using the ecological efficiency – 

nitrate concentration equation defined in Figure 5.6, the target nitrate concentration is 0.293 mg/L. 

5.5.3 Examining the ecological condition of algae and nutrients in Florida Springs Report 

The saturating concentration i.e. the nutrient concentration at which growth was predicted to be elevated by 90% 

above which no effects of nutrient reduction would be expected, for two taxa of common macroalgae that occurred 

in extensive growth were study in a report for the Department in 2007. Surveys of Florida springs indicated that 

almost all springs had macroscopic algae growing in them, an average of 50% of the spring bottoms were covered 

by macroalgae, and the thickness of macroalgal mats was commonly 0.5 m and as thick as 2 m in one spring boil. 

Lyngbya wollei and Vaucheria spp. were the two most common taxa of macroalgae that occurred in areas with 
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extensive growths in the studied springs, however 23 different macroalgal taxa were observed in the spring survey. 

The study involved both field and laboratory components. In the field experiments excessive growth and cover of 

Vaucheria was found at sites with nitrate-nitrite concentrations at or above 0.454 mg/L. In the laboratory 

experiments, the taxa L. wollei and Vaucheria spp. were found to have saturating nitrate concentrations of 0.230 

(mg/L) and 0.261 (mg/L) respectively (Stevenson et al, 2007). The study included 28 springs through out Florida, 

including 8 springs in the SRB. The springs were Madison Blue, Lafayette Blue, Troy, Little River, Turtle, 

Guranato, Fanning, and Manatee Springs (Figure 5.7). 

Figure 5.7 Springs included in the 2007 report 

5.5.4 Relationship between periphyton biomass and cell density and nitrate concentration 

The nitrate target suggested by the Rainbow River study was corroborated by the findings of Hornsby et al. (2000), 

who evaluated periphyton and water quality data collected from the Suwannee River and two tributaries, including 

the Withlacoochee River and Santa Fe River. Much of the length of the Suwannee River was heavily influenced by 

spring inflow. Hornsby et al 2000 showed positive correlations for both periphyton biomass versus nitrate 

concentration and cell density versus nitrate concentration. The functional relationships of periphyton biomass 

(represented as ash free dry mass, or AFDM) versus nitrate concentration and cell density versus nitrate 

concentration are shown in long-term average biomass, cell densities, and nitrate concentrations measured at 13 

stations across the Suwannee River system (including the Withlacoochee River and Santa Fe River) (Figure 5.8). 
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Figure 5.8 Change Point Study Sites 

To further define the nitrate concentration that may significantly impact the periphyton biomass and cell density per 

unit increase of nitrate concentration, the Department contracted with Dr. Xufeng Niu of the Department of 

Statistics, Florida State University, to conduct a change-point analysis for a dataset of 13 long-term periphyton 

monitoring sites over the 1990 to 2007 period provided by the SRWMD. The applied method fits a step function 

through observed data by examining the probability of each data point as the change-point. A nitrate concentration 

change point was identified (at a 5% significant level) if the change of cell density or periphyton biomass caused by 

the nitrate concentration was 3.5 times higher (the T-test critical value) than the standard error of the change of cell 

density or periphyton biomass The identified step-function (the change-point model) was also compared to linear 

regression and non-linear regression models for its goodness-of-fit and the extent of over-fitting based on the 

Bayesian Information Criterion (BIC). For both periphyton cell density and periphyton biomass, change-point step 
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functions were shown to be the best model among the models tested. This supports the use of the change-point 

model identified in the T test. Details of the change-point analyses are provided in Appendix B. For both methods 

based on these analyses the major changes in mean abundance and mean biomass happened at mean a NOx around 

0.441 (Figures 5.9 and 5.10). 

Figure 5.9 Relationship between mean nitrate concentration and mean periphyton biomass from 12 

sampling sites on the Suwannee, Santa Fe, and Withlacoochee Rivers 
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Figure 5.10 Relationship between mean nitrate concentration and mean periphyton cell density from 12 

sampling sites on the Suwannee, Santa Fe, and Withlacoochee Rivers 

When explaining the functional relationship between cell density and nitrate concentration, the change-point step 

function identified two cell density levels (Table 2 in Appendix B). One level is about 218,732 cells/cm2

 (P = 0.00), 

and the other is about 218,732 + 427,894 = 646,626 cells/cm2 (P = 0.0001). In this study, the 218,732 cells/cm2

 was 

considered as the baseline condition under which no significant nitrate impact was detected. The nitrate 

concentration that significantly changed the cell density level from 218,732 cells/cm2

 to 646,626 cells/cm2 was 

identified by the change-point step function as 0.441 mg/L (Table 1 in Appendix B), indicating that, to prevent the 

periphyton cell density from switching to the higher level, the nitrate concentration should not exceed 0.441 mg/L. 

In addition, based on Table 1 and Figure 1 of Appendix B, the cell density switch occurred when the nitrate 

concentration reached 0.441 mg/L. 

The functional relationship between periphyton biomass and nitrate concentration, the change-point step function 

identified two biomass levels (Table 4 in Appendix B). One level is about 1.82 g/m2

 (P= 0.00), and the other level is 

about 1.82+2.97 = 4.79 g/m2

 (P = 0.00). In this study, the 1.82 g/m2 was considered as the baseline condition under 

which no significant nitrate impact was detected. The nitrate concentration that significantly changed the biomass 

level from 1.81 g/m2

 to 4.79 g/m2 was identified by the change-point step function as 0.441 mg/L (Table 3 in 

Appendix B), indicating that, to prevent the periphyton biomass from switching to the higher level, the nitrate 

concentration should not exceed 0.441 mg/L. In addition, based on Table 3 and Figure 4 of Appendix B, the highest 

observed nitrate concentration that allowed the biomass baseline condition was 0.441 mg/L. 
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In the Wekiva River Main Stem and Rock Springs Run TMDL, which was adopted by rule June 8, 2008 Chapter 62-

304, Florida Administrative Code (F.A.C.) included a change point analysis of the Suwannee periphyton data set 

fort the 1990 to 1998 period as one of the line of evidence in target setting 

5.5.5 Target Setting. 

Based on the above lines of evidence, nitrate was primary factor causing elevated growth at levels above 0.230 to 

0.263 mg/L. Nuisance accumulations of Vaucheria occurred at nitrate-nitrite concentrations at or above 0.454 

mg/L. Nitrate concentrations lower than 0.441 mg/L should be appropriate to maintain periphyton cell density and 

biomass at baseline conditions, respectively. An appropriate target (neither under- nor over-protective) should 

include a margin of safety to address uncertainty, as well as to sustain environmental conditions below the 

imbalance point. 

In the change point analysis for mean cell density the mean NO3 was 0.441 mg/L with the test statistic of 7.68 and 

confidence level over 95%. The 95% confidence interval for the change point was between 0.378 mg/L and 0.629 

mg/L of NO3 (Figure 5.11), the lower bound being 0.378 mg/L NO3. It is important to note that the change point 

analysis provides a concentration of nitrate for which change occurs. The TMDL target must be established at a 

level that prevents such a change. Given that we are 95% confident that change occurs between 0.378 mg/L and 

0.629 mg/L of NO3, the department must establish the TMDL threshold below that interval as a preventative 

measure. 

Figure 5.11 Change Point Analyses the 95% confidence interval 

While the change point analysis provided a definitive conclusion that the change in periphyton was related to nitrate, 

the second part is finding the relationship of nitrate concentration to periphyton. The best relationship between 

nitrate and periphyton cell density is an exponential relationship, as shown in Figure 5.12. This relationship can be 

used to define a nitrate target that prevents change. The first approach to finding a target was using the change point 

of 0.441 mg/L to identify an equivalent cell density concentration relative to the central tendency (an exponential 

curve R2

=0.72) of the relationship. Once identified, the nitrate concentration prior to the change point can be 

identified by finding the equivalent Upper 95% Confidence Interval, i.e., a NO3 value of 0.38 mg/L. 
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Figure 5.12 Central Tendency and Upper 95% Confidence interval approach 

In the next approach the same change point of 0.441 was used to find the lower 95% Confidence Interval of cell 

density, which helped establish a margin of safety. The relationship between nitrate and cell density has confidence 

intervals, between which we are 95% confident that the relationship holds. By taking the lower cell density at the 

change point of 0.441 mg/L, we have targeted a more conservative condition in the waterbody. Once identified, we 

again used that cell density to identify a nitrate number prior to the change points by finding the equivalent upper 

95% Confidence Interval (Figure 5.13), i.e., a NO3 value of 0.33 mg/L. 
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Figure 5.13 Upper and Lower 95% Confidence Interval approach. 

Considering that the lower confidence interval value of the change point analysis was 0.378 mg/L and the two 

approaches above found values of 0.38 mg/L and 0.33 mg/L, respectively, an average of the two techniques was 

used to set the target of 0.35 mg/L. 

In conclusion, based on the information currently available, the Department believes that a monthly average nitrate 

concentration of 0.35 mg/L should be sufficiently protective of the aquatic flora or fauna in the Suwannee and Santa 

Fe River Basins. A monthly average is considered to be the appropriate time frame as the Suwannee periphyton 

data set was based on a 28 day deployment and a the response of algae to nutrients is on the order of days to weeks. 

An elevated pollutant concentration in the system alone does not necessarily constitute impairment as long as there 

is no negative response from the local aquatic flora or fauna. Based on information provided above, 0.35 mg/L 

nitrate is the target concentration that will not cause an imbalance in the aquatic flora or fauna in the Suwannee and 

Santa Fe River Basins. The reductions in NO3 will reduce any pollutant impacts associated on DO. Excessive 

growth of algae may result in large diurnal fluctuations in DO due to photosynthesis during the day (oxygen 

production) and respiration during the night (oxygen consumption). The subsequent decomposition of algal biomass 

also consumes large quantities of DO. 
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5.6 Effects of independent variables on Nitrate. 

Algal growth is related to a number of factors including light, water temperature, available nutrients, and flow. 

Certain variables may also be highly correlated with each other (positively or negatively). A Spearman correlation 

matrix was used to assess the correlation between nitrate, algal cell density, algal biomass, and other water quality 

parameters collected in conjunction with periphyton. Nitrate was found to have the highest correlation to both cell 

density and biomass with correlations of 0.797 and 0.699 respectively (Table 5.1). 

Table 5.1 Spearman Correlation on Cell Density and Biomass 

Parameter 

Cell 

Density P value Biomass P value 

NO3NO2 0.797 0 0.699 0 

ALKALINITY 0.67 0 0.49 0.002 

SECCHI 0.591 0 0.382 0.018 

FLOW 0.575 0 0.511 0.001 

CONDUCTIVITY 0.542 0 0.355 0.029 

PH 0.468 0.003 0.346 0.033 

DO 0.242 0.143 0.236 0.154 

SALINITY 0.131 0.459 0.063 0.723 

TN -0.021 0.9 0.131 0.432 

TURBIDITY -0.104 0.533 -0.065 0.697 

NH4 -0.15 0.377 0.114 0.501 

TEMPERATURE -0.174 0.295 -0.18 0.28 

TP -0.211 0.204 -0.098 0.557 

TSS -0.215 0.253 -0.095 0.616 

TKN -0.41 0.011 -0.229 0.168 

COLOR -0.518 0.001 -0.305 0.062 

TOC -0.531 0.001 -0.395 0.014 

Multiple linear regressions were performed to understand the functional relationships between the dependent (cell 

density or algal biomass) and key independent water quality variables. Again nitrate’s correlations were the highest 

when including multiple parameters (Table 5.2). 

Table 5.2 Multiple Regression on Cell Density and Biomass 

 Cell Density Biomass 

Variables Squared multiple R P value Squared multiple R P value

Flow 0.3311 0 0.261 0.001 

Color 0.268 0.001 0.093 0.062 

Temperature 0.03 0.295 0.014 0.478 

NO3NO2 0.621 0 0.475 0 

Color + Temperature 0.292 0.002 0.096 0.172 

Flow + Color 0.513 0 0.311 0.001 

NO3NO2 + Color 0.622 0 0.528 0 

Flow + Temperature 0.513 0 0.283 0.003 

NO3NO2 + Temperature 0.626 0 0.508 0 

NO3NO2 + Flow 0.64 0 0.492 0 

Flow + Color + Temperature 0.554 0 0.32 0.004 

Color + Temperature + NO3NO2 0.627 0 0.57 0 
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Flow + Color + Temperature + NO3NO2 0.641 0 0.574 0 

Selection of variables to include in a regression analysis may result in misleading conclusions if the interactions 

between variables (both dependent and independent) are not considered. The General Linear Model can be used to 

calculate the partial correlations of two variables (a and b) controlling for the effects of a third (c). Table 5.3

illustrates the correlations after applying the General Linear Model by controlling for the effects of flow, color, and 

water temperature. Correlation of Nitrate concentration to cell density and biomass independent of flow, color and 

water temperature was the highest, 0.428 and 0.611 respectively. 

Table 5.3 Partial correlation on Cell density and biomass 

Parameter Cell Density P Value Biomass P Value 

NO3NO2 0.428 0.006 0.611 0 

ALKALINITY 0.397 0.35 0.388 0.025 

CONDUCTIVITY 0.269 0.242 0.229 0.245 

TN 0.147 0.314 0.257 0.111 

NH4 0.015 0.928 0.259 0.121 

PH -0.108 0.386 0.038 0.9 

TURBIDITY -0.323 0.046 -0.207 0.207 

TP -0.389 0.011 -0.168 0.371 

5.7 Setting the Monthly Average Concentration for Nitrate 

As part of the TMDL process, the Department provides a percent reduction goal in the allocation in order to assist 

with implementation. Note that the percent reduction can be calculated in many ways and that achievement of the 

TMDL target (a monthly average of 0.35 mg/L nitrate) may require a different percent reduction depending on when 

and where the measurements are taken. Achievement of the target equates to achievement of the TMDL. However, 

in order to calculate the percent reductions required for each planning unit for this TMDL, the monthly value for 

nitrate was averaged over 1999-2006 and the maximum monthly average was used the as the target for percent 

reduction (Tables 5.1-5.3). 
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Table 5.4 NO3 + NO2 Concentrations (mg/L) in the Main Stem WBIDs over the 1999 - 2006 period, 

Middle Suwannee River 

Year JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC 

1999 0.758 0.313 0.624 0.685 0.735 0.761 0.685 0.656 0.666 0.833 0.671 0.817 

2000 0.854 0.773 0.560 0.205 0.623 0.415 0.471 0.419 0.365 0.514 0.884 0.828 

2001 0.370 0.426 0.407 0.213 0.596 0.546 0.319 0.289 0.687 0.796 0.841 0.843 

2002 0.807 0.716 0.143 0.399 0.609 0.563 0.395 0.503 0.589 0.660 0.509 0.424 

2003 0.204 0.620 0.054 0.138 0.538 0.586 0.339 0.355 0.369 0.986 0.528 0.920 

2004 0.859 0.209 0.270 0.816 0.837 0.800 0.496 0.553 0.051 0.006 0.496 0.384 

2005 0.404 0.581 0.119 0.022 0.350 0.447 0.190 0.190 0.719 0.944 1.021 0.720 

2006 0.114 0.079 0.283 0.946 0.881 0.825 0.772 0.659 2.275 0.548 0.821 0.797 

Monthly 

Average 0.546 0.465 0.308 0.428 0.646 0.618 0.458 0.453 0.715 0.661 0.721 0.716 

Monthly 

Reduction 36% 25% 0% 18% 46% 43% 24% 23% 51% 47% 51% 51% 

Maximum of monthly averages 0.721 

Maximum Percent Reduction 51% 

Table 5.5 NO3 + NO2 Concentrations (mg/L) in the Main Stem WBIDs over the 1999 - 2006 period, Lower 

Suwannee River 

Year JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC 

1999 0.943 0.513 0.662 0.960 0.790 0.505 0.360 0.663 0.666 1.000 0.744 0.905 

2000 0.951 0.881 0.868 0.415 0.492 0.209 0.504 0.766 0.630 0.658 1.048 0.811 

2001 0.510 0.584 0.781 0.244 0.651 0.396 0.463 0.516 0.791 0.690 0.913 0.645 

2002 0.796 0.633 0.274 0.395 0.679 0.351 0.388 0.390 0.580 0.526 0.709 0.536 

2003 0.269 0.740 0.066 0.136 0.641 0.689 0.565 0.423 0.501 0.850 0.709 1.077 

2004 1.080 0.513 0.269 0.805 0.965 0.672 0.643 0.664 0.282 0.128 0.439 0.568 

2005 0.456 0.776 0.509 0.106 0.390 0.600 0.771 0.390 0.872 1.233 1.286 0.910 

2006 0.893 0.493 0.558 1.005 0.992 0.596 1.222 0.644 0.897 0.856 0.855 0.859 

Monthly 

Average 0.737 0.642 0.498 0.508 0.700 0.502 0.614 0.557 0.652 0.743 0.838 0.789 

Monthly 

Reduction 53% 45% 30% 31% 50% 30% 43% 37% 46% 53% 58% 56% 

Maximum of monthly averages 0.838 

Maximum Percent Reduction 58% 

Table 5.6 NO3 + NO2 Concentrations (mg/L) in the Main Stem WBIDs over the 1999 - 2006 period, Lower 

Santa Fe River 

Year JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC 

1999 0.802 0.570 0.642 0.450 0.370 0.563 0.594 0.483 0.398 0.495 0.553 0.598 

2000 0.557 0.498 0.548 0.472 0.473 0.485 0.480 0.397 0.476 0.397 0.542 0.545 

2001 0.170 0.472 0.516 0.465 0.335 0.356 0.396 0.338 0.451 0.418 0.473 0.479 

2002 0.479 0.440 0.387 0.295 0.409 0.369 0.402 0.431 0.471 0.443 0.395 0.387 

2003 0.158 0.377 0.111 0.183 0.477 0.557 0.279 0.276 0.283 0.525 0.570 0.579 

2004 0.589 0.550 0.364 0.536 0.437 0.494 0.416 0.454 0.351 0.024 0.456 0.532 

2005 0.498 0.633 0.473 0.109 0.378 0.665 0.261 0.392 0.606 0.726 0.655 0.683 

2006 0.246 0.402 0.471 0.699 0.639 0.549 0.497 0.529 0.540 0.586 0.563 0.478 

Monthly 

Average 0.437 0.493 0.439 0.401 0.440 0.505 0.416 0.412 0.447 0.452 0.526 0.535 

Monthly 

Reduction 20% 29% 20% 13% 20% 31% 16% 15% 22% 23% 33% 35% 

Maximum of monthly averages 0.535 

Maximum Percent Reduction 35% 

Please note that many springs are also being addressed in this TMDL report and that the nitrate target should also be 

achieved in each of those WBIDs as well. The amount of nitrate data collected in each spring vent is not adequate to 
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calculate a monthly average. However, for information purposes, the table below provides the median nitrate 

concentrations and the percent difference between that number and 0.35 mg/L (Table 5.4). 

Table 5.7 Median NO3 in Springs within the SRB 

WBID Name 

Median NO3 (mg/L) during the 

Verified Period (1999-2006 ) 

Reduction form Target (0.35 

mg/L) 

3422J BRANFORD SPRING 0.895 61% 

3422L RUTH SPRING 4.55 92% 

3422R MANATEE SPRINGS 1.7 79% 

3422S FANNING SPRINGS 4.6 92% 

3422T TROY SPRING 1.865 81% 

3422U ROYAL SPRING 1.35 74% 

3422Z FALMOUTH SPRING 0.91 62% 
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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, or WLAs), nonpoint 

source loads (load allocations, or LAs), and an appropriate margin of safety (MOS), which takes into account any 

uncertainty concerning the relationship between effluent limitations and water quality: 

TMDL = ∑ WLAs + ∑ LAs + MOS 

As discussed earlier, the WLA is broken out into separate subcategories for wastewater discharges and stormwater 

discharges regulated under the NPDES Program: 

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

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

TMDL because (1) the WLA for NPDES stormwater is typically based on the percent reduction needed for nonpoint 

sources and is also accounted for within the LA, and (2) TMDL components can be expressed in different terms (for 

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

typically expressed as mass per day). 

WLAs for stormwater discharges are typically expressed as percent reduction because it is very difficult to quantify 

the loads from MS4s (given the numerous discharge points) and to distinguish the loads from MS4s from other 

nonpoint sources (given the nature of stormwater transport). The permitting of stormwater discharges also differs 

from the permitting of most wastewater point sources. Because stormwater discharges cannot be centrally collected, 

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

instead are required to meet a performance standard of providing treatment to the “maximum extent practical” 

through the implementation of BMPs. 

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

in terms of mass per time (e.g., pounds per day), toxicity, or other appropriate measure. TMDLs for the 

Suwannee and Santa Fe River Basins are expressed in terms of concentration of NO3 (mg/L), and percent reduction 

of nitrate and represent the maximum long-term nitrate concentration the SRB can assimilate and maintain a 

balanced aquatic flora or fauna (Table 6.1). 
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Table 6.1 TMDL components for Suwannee River and Santa Fe River Basins WBIDs, shown as related 

by Planning Units 

Planning Unit Parameter TMD

L WLANPDES wastewater WLANPDES Stormwater LA* MOS

Middle Suwannee 

(WBIDs 3422J, 

3422L, 3422T, 

3422U, 3422Z) 

Nitrate, 

monthly 

average 

0.35 

mg/L N/A N/A 51%** Implicit 

Lower Suwannee 

(WBIDs 3422, 

3422R, 3422S) 

Nitrate, 

monthly 

average 

0.35 

mg/L N/A N/A 58%** Implicit 

Lower Santa Fe 

(WBIDs 3605A, 

3605B, 3605C) 

Nitrate, 

Monthly 

average 

0.35 

mg/L N/A 35%** 35%** Implicit 

*See section 5.6, Tables 5.1-5.3 for description of percent reduction calculation. If the overall TMDL (0.35 mg/L) is the basis for 

the percent reduction and the percent reduction may be different based on variations in time and space. Achievement of the 

TMDL constitutes achievement of the percent reduction. 

**Springs located in with in the different Planning Units will have varying percent reduction Load Allocations. However, data 

do not exist at this time to calculate a monthly average (see Figure 5.10) 

The percent load reductions listed on Table 6.1 were established to achieve the monthly average nitrate 

concentration of 0.35 mg/L. While these percent reductions are the expression of the TMDL that will be 

implemented, EPA1

 recommends that all TMDLs and associated load allocations and wasteload allocations include 

a daily time increment in conjunction with other appropriate temporal expressions that may be necessary to 

implement the relevant water quality standard. Daily maximum concentration target for nitrate was established 

using the following equation2

, which assumes that the nitrate data distributions are lognormal in Suwannee and 

Santa Fe River Basins: 

 MDL = LTA * exp(Zpσy – 0.5σy

2

) 

σy = sqrt(ln(CV2

 + 1)) 

Where 

 LTA = long-term average (0.35 mg/L) 

 Zp = pth percentage point of the standard normal distribution, at 95% (Zp =1.645) 

σ = standard deviation 

 CV = coefficient of variance 

For the daily maximum nitrate concentration, it was assumed that the average monthly target concentration should 

be the same as the average daily concentration. Also, assuming the target data set will have the same CV as the 

existing measured data set and allowing 10% exceedance, the daily maximum nitrate concentrations for Middle 

Suwannee, Lower Suwannee and Lower Santa Fe Rivers are 1.19, 0.76, and 0.77 mg/L, respectively. The nitrate 

daily maximum target was chosen as the final daily maximum nitrate target for the Suwannee and Santa Fe River 

Basins (Table 6.2). The means, STDEVs, and CVs of nitrate concentrations of different water segments are listed in 

Table 6.2. 

 1

 November 2006 U. S. Environmental Protection Agency (USEPA 2006) Memorandum “Establishing TMDL “Daily” Loads in 

Light of the Decision by the U.S. Court of Appeals for the D.C. Circuit in Friends of the Earth, Inc. v. EPA et. al., 

No.05-5015 (D.C. Cir. 2006) and Implications for NPDES permits.” 2

 EPA, “Options for Expressing Daily Load in TMDL (The Option),” June, 2007. 
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Table 6.2 Daily maximum for target nitrate concentration (mg/L) 

Statistics 

Middle 

Suwannee 

Lower 

Suwannee 

Lower Santa 

Fe 

Mean 0.64 0.65 0.48 

STDEV 1.055 0.4 0.3 

CV 1.64 0.62 0.63 

Daily Maximum to achieve long term 

average (0.35 mg/L) 1.19 0.76 0.77 

It should be emphasized that these daily maximum targets were developed for illustrative purposes. Implementation 

of the TMDL will be based on the monthly average concentration targets. 

6.2 Load Allocation 

Because no target loads were explicitly calculated in this TMDL report due to the lack of flow data at the outlet of 

each stream segment, TMDLs are represented as the percent reduction required to achieve the nitrate target. The 

percent reduction assigned to all the nonpoint sources areas (LA) are the same as those defined for the TMDL 

percent reduction. To achieve the annual average nitrate target of 0.35 mg/L in the Suwannee and Santa Fe River 

basins, the nitrate loads from the nonpoint source related to Middle Suwannee, Lower Suwannee and Santa Fe rivers 

need to be reduced by 51%, 58% and 35%, respectively. The target long-term average is 0.35 mg/L and the percent 

reduction represent an estimate of the maximum amount of reduction required to meet the target. It may be possible 

to the target before achieving the percent reductions. 

6.3 Wasteload Allocation 

6.3.1 National Pollutant Discharge Elimination System Stormwater Discharges 

Because no information was available to the Department at the time this analysis was conducted regarding the 

boundaries and locations of all the NPDES stormwater dischargers, the exact stormwater nitrate loading from MS4 

areas were not explicitly estimated. Within the Santa Fe River drainage basin, Alachua County has a Phase II MS4 

permit (FLR04E005), the Florida Department of Transportation (FDOT) District 2 holds a Phase II (FLR04E018), 

the City of Gainesville holds a Phase II (FLR04E006) and the University of Florida holds a Phase II(FLR04E067. 

The wasteload allocations for each of the MS4s are the same percent nitrate reduction required for the LA assigned 

to the nonpoint sources in the river segments that belong to each county and municipality. 

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 is not responsible for reducing other nonpoint 

source loads within its jurisdiction. 

6.4 Margin of Safety 

Consistent with the recommendations of the Allocation Technical Advisory Committee (Department, February 

2001), an implicit MOS was used in the development of this TMDL. The MOS was addressed in several aspects of 

the analyses. For example, the nitrate target was established based on the most conservative concentration from the 

four lines of evidence (Section 5.5). Requiring that the 0.35 mg/L target be met every month should result in the 

nitrate concentration to be even lower than the target concentration during the summer algal growth season based on 

seasonal analysis on the nitrate concentration, and therefore adds to the margin of safety. In addition, when 

estimating the required percent reduction to achieve the water quality target, the highest long-term monthly averages 

of measured nitrate concentrations, instead of average long-term monthly averages, were chosen to represent the 

existing condition. This will make estimating the required percent load reduction more conservative and therefore 

add to the margin of safety. 
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6.5 Recommendations for Further Studies 

As described in Chapter 1, the watershed approach is implemented using a cyclical management process that rotates 

through the state over a 5-year cycle. Following completion of the TMDL phase, subsequent phases involve the 

development of a basin management action plan and implementation. There are a number of studies that are 

recommended to improve our understanding of this complex system and ensure that implementation activities are 

resulting in water quality improvements. Continued work to delineate springsheds and source identification within 

those springsheds is important. Ongoing development, implementation, and assessment of BMPs will also be 

critical to the long-term success in improving water quality. In five years when the next assessment cycle of the 

Suwannee River Basin occurs water quality information collected as part of the monitoring program will be 

essential. 
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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 BMAP. This document will be developed over the next two years 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. 

The Department recognizes that this TMDL value still represents a monumental challenge to the local community 

that will take significant time, coordination, and resources to address. The Department is committed to working 

with the Suwannee River Water Management District and local stakeholders to address these challenges. A unique 

advantage in these basins is the existence of the Suwannee River Partnership, a proven organization that has 

proactively addressed water quality issues over the past 10 years with advances in pollution reduction, scientific 

understanding, and community awareness. The Department maintains that this Partnership is on the right path and 

should continue moving in that direction after the establishment of this TMDL. The Partnership will play a 

significant role the Basin Management Action Plan process. 
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References 

Alexander, Richard B., and Smith, Richard A., 1990, County-level estimates of nitrogen and phosphorus 

fertilizer use in the United States, 1945 to 1985: U.S. Geological Survey Open-File Report 90-130, 12 p. 

Battaglin, William A. and Goolsby, Donald A., 1994, Spatial Data in Geographic Information System Format 

on Agricultural Chemical Use, Land Use, and Cropping Practices in the United States, U.S. Geological 

Survey Water-Resources Investigations Report 94-4176 

Cowell, B. C. and C. J. Dawes. 2004. Growth and nitrate-nitrogen uptake by the cyanobacterium Lyngbya 

wollei. J. Aquatic Plant Management 42: 69-71. 

D.C. Cir. (United States Court of Appeals for the District of Columbia). 2006. Friends of the Earth, Inc.v. 

EPA, et al. No. 05-5015. 

Department of Health and Rehabilitative Services (HRS), State of Florida 1993. Suwannee River Floodplain 

Onsite Sewage Disposal Systems Inventory, Annual Report 1993 

Department of Health and Rehabilitative Services (HRS), State of Florida 1994. Suwannee River Floodplain 

Onsite Sewage Disposal Systems Inventory, Final Report 1994 

Florida Administrative Code. Chapter 62-302, Surface water quality standards. 

Florida Administrative Code. Chapter 62-303, Identification of impaired surface waters. 

Florida Watershed Restoration Act. Chapter 99-223, Laws of Florida. 

Florida Department of Environmental Regulation (FDER). 1985. Limnology of the Suwannee River, 

Florida. Report by the Biology Section, Division of Environmental Programs. Tallahassee, FL. 

Florida Department of Environmental Protection. 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. Available: 

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

Florida Department of Environmental Protection (FDEP). 2001. Basin status report: Suwannee. 

Tallahassee, FL. 

Florida Department of Health, Division of Environmental Health, 2007, Onsite Sewage, Available 

http://www.doh.state.fl.us/environment/programs/ehgis/EhGisDownload.htm

Ham, L.K. and H.H. Hatzell. 1996. Analysis of nutrients in the surface waters of the Georgia-Florida 

Coastal plain study unit, 1970-91. U.S. Dept. of the Interior, U.S. Geological Survey, Denver, CO. 

Harper, H. H. and D. B. Baker. 2003. Evaluation of alternative stormwater regulations for southwest 

Florida. Submitted to: Water Enhancement & Restoration Coalition, Inc. Prepared by Environmental 

Research & Design, Inc. 

Hornsby, D. and R. Mattson. 1998. Surfacewater quality and biological monitoring annual report 1997. 

Water Resour. Rep. WR98-03. Suwannee River Water Management District, LiveOak, FL. 
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Hornsby, D. and R. Ceryak. 1999. Springs of the Suwannee River Basin in Florida. Suwannee River Water 

Management District Report, WR99-02. Live Oak, FL. 

Hornsby, D., R. A. Mattson, and T. Mirti. 2000. Surfacewater quality and biological monitoring. Annual 

Report. 1999. Suwannee River Water Management District Technical Report WR-00-04. iv, 148 pp. 

Hornsby, D. 2007. Influences On The Distribution And Occurrence Of Nitrate-Nitrogen And Total 

Phosphorus In The Water Resources Of The Suwannee River Water Management District, University of 

Florida, 262 pp. 

Katz, B.G. 1992. Hydrochemistry of the Upper Floridan aquifer in Florida. U.S. Geological Survey Water 

Resources Investigations Report, 91-4196. Tallahassee, FL. 

Katz, B.G., H.D. Hornsby, J.F. Bohlke, and M.F. Mokray. 1999. Sources and chronology of nitrate 

contamination in spring waters, Suwannee River basin, Florida. U.S. Geological Survey, Water 

Resources Investigations Report, 99-4252. Tallahassee, FL. 

Mattson, R. A., E. F. Lowe, C. L. Lippincott, and L. Battoe. 2006. Wekiva River and Rock Springs Run 

pollutant load reduction goals. Report to the Florida Department of Environmental Protectcion. St. 

Johns River Water Management District, Palatka, FL. 

Oaksford, E.T., 1994, National Water-Quality Assessment Program - preliminary results: agricultural 

chemicals in the Suwannee River basin, Georgia-Florida Coastal Plain study unit: U.S. Geological 

Survey OFR 94-103 

Pittman, J.R., H.H. Hatzell, and E.T. Oaksford. 1997. Spring contributions to water quality and nitrate 

loads in the Suwannee River during base flow in July 1995. U.S. Geological Survey Water-Resources 

Investigations Report, 97-4152. Tallahassee, FL. 

Quinlan, E. B. 2003. Consequences of Nutrient Loading In The Suwannee River And Estuary, Florida, 

USA. University of Florida, 152pp. 

Stevenson, R. J, et al. 2007. Ecological condition of algae and nutrients in Florida Springs. Final Report to 

the Florida Department of Environmental Protection, Tallahassee, FL. 58pp. 

United States Census Bureau. Census 2007, Available at http://www.census.gov/

United States Department of Agriculture, National Agriculture Statistics Service, USDA 2007. Available at 

http://www.nass.usda.gov/Statistics_by_State/Florida/Publications/Livestock_and_Poultry/index.asp

United States Environmental Protection Agency. 2006a. Establishing TMDL “Daily” Loads in Light of the 

Decision by the U.S. Court of Appeals for the D.C. Circuit in Friends of the Earth, Inc. v. EPA, et al., 

No.05-5015, (April 25, 2006) and Implications for NPDES permits. Memorandum from Benjamin 

Grumbles, assistant administrator, Office of Water. U.S. Environmental Protection Agency, 

Washington, DC. 

United States Environmental Protection Agency. 2007. Options to expressing daily loads in TMDL (draft). 

Office of Wetlands, Oceans, and Watersheds. 
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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. In 1994, the Department’s stormwater treatment 

requirements were integrated with the stormwater flood control requirements of the state’s water management 

districts, along with wetland protection requirements, into the Environmental Resource Permit regulations. 

Chapter 62-40, F.A.C., also requires the water management districts to establish stormwater pollutant load reduction 

goals (PLRGs) and adopt them as part of a SWIM plan, other watershed plan, or rule. When applicable, stormwater 

PLRGs may be a major component of the load allocation part of a TMDL. 

In 1987, the U.S. Congress established Section 402(p) as part of the federal Clean Water Act Reauthorization. This 

section of the law amended the scope of the federal NPDES permitting program to designate certain stormwater 

discharges as “point sources” of pollution. The EPA promulgated regulations and began implementing the Phase I 

NPDES stormwater program in 1990. These stormwater discharges include certain discharges that are associated 

with industrial activities designated by specific standard industrial classification (SIC) codes, construction sites 

disturbing 5 or more acres of land, and master drainage systems of local governments with a population above 

100,000, which are better known as municipal separate storm sewer systems (MS4s). However, because the master 

drainage systems of most local governments in Florida are interconnected, the EPA implemented Phase I of the MS4 

permitting program on a countywide basis, which brought in all cities (incorporated areas), Chapter 298 urban water 

control districts, and the Florida Department of Transportation throughout the 15 counties meeting the population 

criteria. The Department received authorization to implement the NPDES stormwater program in 2000. 

An important difference between the federal NPDES and the state’s stormwater/environmental resource permitting 

programs is that the NPDES Program covers both new and existing discharges, while the state’s program focuses on 

new discharges only. Additionally, Phase II of the NPDES Program, implemented in 2003, expands the need for 

these permits to construction sites between 1 and 5 acres, and to local governments with as few as 1,000 people. 

While these urban stormwater discharges are now technically referred to as “point sources” for the purpose of 

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

facility, as are other point sources of pollution such as domestic and industrial wastewater discharges. It should be 

noted that all MS4 permits issued in Florida include a re-opener clause that allows permit revisions to implement 

TMDLs when the implementation plan is formally adopted. 
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Appendix B Change Point Analysis of the Suwannee River 

Algal Data 
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Appendix C Historic Fertilizer Sales 

Table C.1 Historic Total Nitrogen Sales 1945-1991 (Tons) 

 County Year Alachua Baker Bradford Columbia Dixie Gilchrist Hamilton Jefferson 

Lafayette Levy Madison Suwannee Taylor Union 

1945 672 43 83 389 33 295 334 343 162 401 510 680 45 95 

1946 714 46 88 414 35 314 355 364 172 426 542 722 48 101 

1947 696 45 86 403 34 306 346 355 168 415 528 704 47 98 

1948 626 40 77 363 31 275 312 320 151 374 476 634 42 89 

1949 620 40 76 360 30 273 309 317 150 370 471 628 42 88 

1950 762 49 94 442 37 335 380 389 184 455 579 772 51 108 

1951 943 61 116 547 46 415 469 481 227 563 716 955 63 133 

1952 1036 67 127 601 50 456 516 529 250 619 787 1049 69 146 

1953 1206 78 148 699 59 530 600 615 291 720 916 1221 81 170 

1954 1320 85 162 765 64 580 657 673 318 788 1002 1336 88 186 

1956 1561 101 192 904 76 686 777 796 376 932 1185 1580 105 221 

1957 1800 116 221 1043 88 791 896 919 434 1075 1367 1822 121 254 

1958 1879 121 231 1089 91 826 935 959 453 1122 1427 1902 126 266 

1959 1901 123 234 1101 93 835 946 970 458 1135 1443 1924 127 269 

1960 2078 134 256 1204 101 914 1034 1060 501 1241 1578 2103 139 294 

1961 2177 140 268 1262 106 957 1084 1111 525 1300 1653 2204 146 308 

1962 2235 144 275 1295 109 982 1112 1140 538 1334 1697 2262 150 316 

1963 2216 143 273 1284 108 974 1103 1130 534 1323 1682 2243 149 313 

1964 2350 152 289 1362 114 1033 1170 1199 566 1403 1784 2378 158 332 

1965 2547 164 313 1476 124 1120 1268 1300 614 1521 1934 2578 171 360 

1966 2686 173 330 1557 131 1181 1337 1370 647 1604 2039 2719 180 380 

1967 2518 162 310 1459 123 1107 1254 1285 607 1504 1912 2549 169 356 

1968 2785 180 343 1614 136 1224 1386 1421 671 1663 2114 2819 187 394 

1969 3265 211 402 1892 159 1435 1625 1666 787 1949 2479 3304 219 461 

1970 3461 223 426 2006 169 1522 1723 1766 834 2067 2628 3503 232 489 

1971 3317 214 408 1922 162 1458 1651 1692 799 1981 2519 3358 222 469 

1972 3613 233 444 2094 176 1588 1799 1844 871 2158 2743 3657 242 511 

1973 3802 245 468 2204 185 1671 1893 1940 916 2271 2887 3849 255 537 

1974 3840 248 472 2225 187 1688 1911 1959 925 2293 2915 3887 257 543 

1975 3394 219 417 1967 165 1492 1689 1732 818 2027 2577 3435 228 480 

1976 3990 257 491 2312 194 1754 1986 2036 961 2383 3029 4038 267 564 

1977 5260 286 1359 2971 228 2823 2046 1911 1404 3524 4659 5162 0 891 

1978 4906 266 1268 2771 212 2633 1908 1782 1310 3286 4345 4814 0 831 

1979 5475 297 1415 3093 237 2939 2129 1989 1462 3668 4849 5373 0 928 

1980 5279 287 1364 2982 229 2833 2053 1918 1409 3537 4676 5180 0 895 

1981 3984 494 349 1935 176 2150 1868 2610 1083 2762 4294 5781 245 769 

1982 3773 468 330 1832 167 2036 1769 2471 1026 2616 4067 5474 232 729 

1983 3693 458 323 1794 163 1993 1731 2419 1004 2560 3981 5359 227 713 

1984 3787 470 332 1839 167 2044 1775 2481 1029 2626 4082 5495 233 731 
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1985 3417 424 299 1660 151 1844 1602 2238 929 2369 3683 4958 210 660 

1986 2538 392 275 1032 58 1183 1243 1923 801 1465 1235 2859 169 523 

1987 3190 493 346 1298 73 1487 1563 2417 1007 1842 1552 3594 213 658 

1988 2551 394 277 1038 58 1189 1250 1932 805 1472 1241 2873 170 526 

1989 2750 425 298 1119 63 1282 1347 2083 868 1587 1338 3098 183 567 

1990 2798 432 304 1138 64 1304 1371 2120 883 1615 1361 3152 187 577 

1991 2648 409 287 1077 60 1235 1297 2006 836 1529 1288 2983 177 546 

Table C.2 Historic Total Phosphorus Sales 1945-1991 (Tons) 

County 

Year Alachua Baker Bradford Columbia Dixie Gilchrist Hamilton Jefferson Lafayette Levy Madison Suwannee Taylor Union 

1945 426 27 52 247 21 187 212 217 103 254 323 431 29 60 

1946 479 31 59 278 23 211 239 245 116 286 364 485 32 68 

1947 501 32 62 290 24 220 250 256 121 299 381 507 34 71 

1948 415 27 51 241 20 183 207 212 100 248 315 420 28 59 

1949 432 28 53 250 21 190 215 220 104 258 328 437 29 61 

1950 490 32 60 284 24 215 244 250 118 292 372 496 33 69 

1951 544 35 67 315 27 239 271 278 131 325 413 551 36 77 

1952 586 38 72 339 29 258 292 299 141 350 445 593 39 83 

1953 606 39 75 351 30 266 302 309 146 362 460 613 41 86 

1954 612 39 75 355 30 269 305 312 147 365 464 619 41 86 

1955 610 39 75 354 30 268 304 311 147 364 463 618 41 86 

1956 674 43 83 390 33 296 335 344 162 402 511 682 45 95 

1957 745 48 92 432 36 328 371 380 180 445 566 754 50 105 

1958 732 47 90 424 36 322 364 373 176 437 556 741 49 103 

1959 717 46 88 416 35 315 357 366 173 428 545 726 48 101 

1960 722 47 89 418 35 317 359 368 174 431 548 730 48 102 

1961 739 48 91 428 36 325 368 377 178 441 561 748 50 104 

1962 730 47 90 423 36 321 363 372 176 436 554 739 49 103 

1963 731 47 90 424 36 321 364 373 176 437 555 740 49 103 

1964 782 50 96 453 38 344 389 399 189 467 594 792 52 111 

1965 2547 164 313 1476 124 1120 1268 1300 614 1521 1934 2578 171 360 

1966 2686 173 330 1557 131 1181 1337 1370 647 1604 2039 2719 180 380 

1967 2518 162 310 1459 123 1107 1254 1285 607 1504 1912 2549 169 356 

1968 2785 180 343 1614 136 1224 1386 1421 671 1663 2114 2819 187 394 

1969 3265 211 402 1892 159 1435 1625 1666 787 1949 2479 3304 219 461 

1970 3461 223 426 2006 169 1522 1723 1766 834 2067 2628 3503 232 489 

1971 3317 214 408 1922 162 1458 1651 1692 799 1981 2519 3358 222 469 

1972 3613 233 444 2094 176 1588 1799 1844 871 2158 2743 3657 242 511 

1973 3802 245 468 2204 185 1671 1893 1940 916 2271 2887 3849 255 537 

1974 3840 248 472 2225 187 1688 1911 1959 925 2293 2915 3887 257 543 

1975 3394 219 417 1967 165 1492 1689 1732 818 2027 2577 3435 228 480 

1976 812 52 100 470 40 357 404 414 196 485 616 821 54 115 
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1977 1043 57 269 589 45 560 405 379 278 698 923 1023 0 177 

1978 1026 56 265 579 44 550 399 373 274 687 908 1006 0 174 

1979 1178 64 305 666 51 632 458 428 315 789 1044 1156 0 200 

1980 1030 56 266 582 45 553 400 374 275 690 912 1011 0 175 

1981 752 93 66 365 33 406 352 493 204 521 810 1091 46 145 

1982 693 86 61 336 31 374 325 454 188 480 746 1005 43 134 

1983 675 84 59 328 30 364 316 442 183 468 727 979 42 130 

1984 712 88 62 346 31 384 334 466 194 494 768 1033 44 138 

1985 1057 163 115 430 24 493 518 801 333 610 514 1190 71 218 

1986 1032 160 112 420 24 481 506 782 326 596 502 1163 69 213 

1987 1432 221 155 582 33 668 701 1085 452 827 697 1613 96 295 

1988 1055 163 114 429 24 492 517 800 333 609 513 1189 70 218 

1989 1089 168 118 443 25 508 534 825 344 629 530 1227 73 225 

1990 1150 178 125 468 26 536 564 872 363 664 560 1296 77 237 

1991 1055 163 114 429 24 492 517 799 333 609 513 1188 70 218 

Table C.3 1998 to 2007 Fertilizer Sales (Tons) 

MULTIPLE NUTRIENT ALL FERTILIZERS 

Year County 

TOTAL 

FERTILIZER 

TOTAL 

SINGLE 

TOTAL 

MULTI 

ALL 

OTHER 

TOTAL 

N 

TOTAL 

P2O5 

TOTAL 

K2O 

TOTAL 

N 

TOTAL 

P2O5 

TOTAL 

K2O 

 2 3 4 5 6 7 8 9 10 11 

1998 ALACHUA 12,781 3,740 8,637 404 1,171 546 879 2,081 563 1,113 

1998 BAKER 3,675 1,436 2,224 13 404 663 90 1,045 664 102 

1998 BRADFORD 2,886 479 2,334 72 368 122 320 523 122 323 

1998 COLUMBIA 13,964 2,391 11,083 489 1,499 830 1,336 2,032 830 1,505 

1998 DIXIE 2,698 235 2,446 16 72 43 58 129 43 58 

1998 GILCHRIST 22,906 3,260 19,217 428 2,887 998 1,916 3,489 998 2,016 

1998 HAMILTON 7,687 3,121 4,453 112 417 295 749 1,350 295 780 

1998 JEFFERSON 13,307 5,647 7,619 41 1,058 710 1,077 2,358 710 1,092 

1998 LAFAYETTE 14,023 5,729 8,293 0 1,068 517 1,313 2,241 517 1,729 

1998 LEVY 22,365 4,750 14,630 2,984 2,289 782 1,880 3,621 784 1,921 

1998 MADISON 9,418 3,470 4,664 1,283 651 283 749 1,528 284 1,016 

1998 SUWANNEE 37,979 16,922 19,259 1,796 2,561 1,355 3,303 6179 1370 4775 

1998 TAYLOR 1,218 386 831 1 139 211 68 226 211 91 

1998 UNION 9,169 2,774 6,356 39 1,119 751 725 1804 753 753 

 

1999 ALACHUA 18,662 5,390 11,859 1,963 1,897 628 1,513 2,995 638 1,911 

1999 BAKER 1,913 105 1,769 39 356 377 87 383 377 96 

1999 BRADFORD 3,960 1,091 2,831 87 398 133 269 589 133 295 

1999 COLUMBIA 5,385 1,229 3,681 978 596 219 997 826 219 955 

1999 DIXIE 1,585 69 1,065 950 72 27 93 90 29 95 

1999 GILCHRIST 10,690 1,957 7,557 1,175 1,272 320 689 1,675 320 739 

1999 HAMILTON 6,793 1,368 5,922 1 565 956 585 922 956 699 

1999 JEFFERSON 11,993 9,059 7,818 70 1,057 715 1,020 2,163 715 1,030 

1999 LAFAYETTE 6,959 2,892 3,965 101 529 207 592 1,126 208 715 

1999 LEVY 31,609 9,887 16,291 10,926 2,809 1,320 2,031 9,195 1,320 2,052 

1999 MADISON 7,926 2,708 3,570 1,697 510 226 552 1,239 226 675 
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1999 SUWANNEE 26,202 11,256 11,858 3,087 1,617 768 1,986 3,726 771 3,006 

1999 TAYLOR 1,196 353 805 37 139 210 57 205 210 58 

1999 UNION 9,023 2,192 6,597 232 1,179 502 851 1,616 539 869 

 

2000 ALACHUA 26,662.60 4,744.95 20,592.11 1,325.54 2,806.08 1,158.75 1,925.11 4,142.84 1,195.91 2,250.87 

2000 BAKER 3,090.66 539.6 2,514.86 36.2 563.88 535.17 172.71 693.04 535.79 303.62 

2000 BRADFORD 5,137.27 721.86 4,387.20 28.2 532.6 200.54 375.26 697.59 200.61 386.39 

2000 COLUMBIA 8,408.64 2,872.37 5,203.43 332.84 791.79 343.99 794.53 1,686.41 344.99 828.48 

2000 DIXIE 5,661.71 900.97 2,845.36 1,915.37 445.38 482.45 284.41 573.4 498.56 627.16 

2000 GILCHRIST 13,071.27 3,115.17 8,994.55 961.55 1,251.16 471.3 1,102.84 1,863.71 477.15 1,313.05 

2000 HAMILTON 10,983.74 1,884.70 5,973.21 3,125.84 425.52 325.04 705.98 943.07 325.04 771.68 

2000 JEFFERSON 11,113.62 3,793.37 7,198.65 121.6 965.1 705.93 1,019.25 1,758.99 726.86 1,027.49 

2000 LAFAYETTE 6,783.95 3,516.23 3,232.82 34.9 430.08 252.2 475.76 1,144.97 254.27 547.02 

2000 LEVY 19,323.26 3,230.02 12,375.32 3,717.92 2,281.22 897.3 1,467.79 3,279.49 897.4 1,504.51 

2000 MADISON 8,801.44 3,492.42 3,826.20 1,482.82 543.62 261.66 591.15 1,443.78 261.91 809.19 

2000 SUWANNEE 25,851.61 11,820.71 11,340.19 2,690.71 1,547.15 850.3 1,891.25 3,764.51 852.33 2,985.10 

2000 TAYLOR 2,229.70 458.66 1,623.69 147.35 272.41 537.35 68.89 413.79 538.29 69.59 

2000 UNION 13,512.84 3,365.69 9,580.77 566.37 1,567.02 1,117.36 1,319.70 2,453.21 1,118.11 1,440.03 

 

2001 ALACHUA 20,005.64 4,088.52 14,839.07 1,078.06 2,275.42 953.34 1,524.39 2,932.95 957.13 1,975.97 

2001 BAKER 3,092.87 355.27 2,572.47 165.13 581.53 258.65 201.96 606.99 259.37 346.8 

2001 BRADFORD 4,019.25 760.37 1,676.19 1,582.69 270.95 92.84 244.95 426.86 93.54 256.45 

2001 COLUMBIA 7,916.65 1,839.24 4,752.24 1,325.17 774.16 300.54 670.31 1,062.57 301.32 689.34 

2001 DIXIE 5,139.28 876.52 1,687.85 2,574.90 232.17 182.97 241.77 297.94 199.51 540.73 

2001 GILCHRIST 13,680.68 2,646.48 10,504.05 530.15 1,694.74 441.66 1,505.60 2,045.48 441.86 1,901.06 

2001 HAMILTON 4,639.82 1,221.10 3,418.72 292.09 246.6 468.34 585.71 249.76 520.57 

2001 JEFFERSON 12,194.07 4,146.35 8,003.31 44.41 1,126.05 775.4 1,193.55 2,013.91 781.51 1,239.59 

2001 LAFAYETTE 6,762.37 3,250.60 3,382.77 129 467.92 249.35 485.49 849.31 249.81 594.44 

2001 LEVY 20,399.59 2,799.72 12,525.82 5,074.06 2,309.19 859.05 1,582.49 2,953.30 860.02 1,609.57 

2001 MADISON 8,349.64 2,932.99 4,401.34 1,015.31 633.52 295.91 673.82 1,426.49 295.91 769.14 

2001 SUWANNEE 23,851.11 9,711.88 10,444.98 3,694.25 1,332.49 768.72 1,758.33 2,977.85 771.19 2,462.08 

2001 TAYLOR 1,822.01 544.09 1,248.53 29.38 202.54 312.98 82.69 369.84 314.26 86.37 

2001 UNION 9,656.93 2,198.15 7,394.72 64.06 1,378.33 646.34 932.94 1,788.96 647.77 970.22 

 

2002 ALACHUA 20,080.43 2,928.39 15,291.77 1,860.27 2,015.56 781.74 1,659.21 2,568.35 786.73 1,931.12 

2002 BAKER 1,441.70 127.19 1,012.14 302.37 224.06 81.19 84.81 259.75 81.95 93.89 

2002 BRADFORD 4,591.10 979.24 3,331.55 280.31 360.3 135.32 229.9 573.24 136.88 260.16 

2002 COLUMBIA 7,705.33 1,636.31 5,669.12 399.9 675.22 378.06 1,241.80 1,005.92 378.9 1,312.80 

2002 DIXIE 4,976.72 1,028.67 1,750.63 2,197.41 222.91 188.67 302.01 192.28 203.53 681.82 

2002 GILCHRIST 20,624.49 3,201.74 17,006.24 416.51 2,704.16 976.69 2,744.04 3,455.84 977.08 2,976.24 

2002 HAMILTON 6,014.35 2,006.86 3,952.09 55.4 382.87 303.21 630.85 935.63 303.22 702.72 

2002 JEFFERSON 11,821.07 3,672.10 7,897.27 251.7 1,129.52 778.55 1,153.94 2,013.98 799.85 1,192.49 

2002 LAFAYETTE 6,839.72 3,077.00 3,511.52 251.2 472 222.34 593.35 996.99 222.35 1,040.15 

2002 LEVY 22,831.88 3,499.43 14,209.69 5,122.77 2,222.37 926.85 2,215.00 3,269.09 928.86 2,331.36 

2002 MADISON 9,881.17 2,954.91 4,300.51 2,625.75 625.03 241.35 707.07 1,453.08 241.38 764.49 

2002 SUWANNEE 25,902.13 11,596.61 11,136.20 3,169.33 1,502.39 832.06 1,899.49 3,720.99 833.71 2,847.64 
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2002 TAYLOR 2,435.42 1,297.48 1,077.90 60.04 183.12 318.66 66.2 639.38 319.5 69.68 

2002 UNION 6,564.75 1,022.01 5,411.96 130.78 1,010.51 443.5 721.4 1,215.74 444.2 741.53 

 

2003 ALACHUA 20,509.71 2,990.79 15,340.13 2,178.79 1,656.53 651.59 1,239.09 2,228.36 657.3 1,509.96 

2003 BAKER 2,009.40 597.49 1,294.90 117 250.86 101.97 129.87 444.75 102.54 138.42 

2003 BRADFORD 3,981.11 1,191.10 2,613.80 176.2 375.5 132.18 197.18 622.21 132.72 255.63 

2003 COLUMBIA 8,426.29 2,265.51 5,763.52 397.27 864.41 368.57 944.63 1,280.97 369.29 1,078.33 

2003 DIXIE 4,682.94 453.51 1,994.76 2,234.67 239.46 112.91 259.31 315.03 123.82 340.81 

2003 GILCHRIST 20,633.75 3,102.58 15,858.47 1,672.70 2,033.35 722.56 2,383.56 2,585.30 724.87 2,824.91 

2003 HAMILTON 6,408.93 2,290.06 4,117.67 1.2 427.02 321.21 649.87 984.39 321.22 829.28 

2003 JEFFERSON 12,739.43 3,516.53 8,737.67 485.23 1,241.63 824.3 1,299.87 2,134.68 847.8 1,341.82 

2003 LAFAYETTE 6,993.84 2,421.19 3,986.34 586.31 554.18 215.98 638.84 1,036.63 215.98 816.06 

2003 LEVY 29,202.91 4,860.48 16,699.40 7,643.03 2,543.42 1,253.56 2,589.33 3,736.76 1,256.30 2,667.93 

2003 MADISON 10,547.48 3,290.26 4,795.68 2,461.54 711.59 323.78 791.61 1,575.91 324 927.61 

2003 SUWANNEE 27,409.48 13,228.87 11,622.74 2,557.86 1,514.68 819.04 1,940.52 3,963.35 819.55 3,089.99 

2003 TAYLOR 1,225.73 526.41 620.17 79.16 90.47 29.36 84.66 255.56 29.53 86.17 

2003 UNION 13,114.29 3,963.25 9,014.54 136.5 1,277.80 997.29 1,548.59 2,186.99 997.89 1,630.59 

 

2004 ALACHUA 17710.18 2656.63 11365.42 3688.12 1533.72 609.46 1621.71 2045.12 617.06 1850.77 

2004 BAKER 1481.29 120.67 1149.21 211.41 175.93 102.89 147.8 209.67 103.56 153.06 

2004 BRADFORD 4199.62 1305.72 2559.45 334.45 324.21 118.61 252.12 565.25 119.5 323.74 

2004 COLUMBIA 8858.26 2163.61 5351.2 1343.45 832.69 300.08 730.05 1260.63 301.04 782.47 

2004 DIXIE 7152.02 752.63 3287.43 3111.97 373.75 263.65 349.06 502.38 276.49 417.14 

2004 GILCHRIST 20870.45 1988.79 14520.8 4360.86 1982.99 807.62 2352.13 2333.24 808.04 2618.73 

2004 HAMILTON 6278.84 1862.18 4266.99 149.67 361.45 372.82 677.71 742.97 448.99 741.8 

2004 JEFFERSON 12434.2 2896.59 9240.59 297.02 1280.49 923.36 1325.35 2067.58 924.25 1467.61 

2004 LAFAYETTE 7904.63 2920.58 4646.6 337.44 617.9 257.18 687.15 1256.13 301.34 988.5 

2004 LEVY 26662.24 4604.19 17167.49 4890.56 2578.25 1151.55 2746.35 3659.31 1157.25 3025.11 

2004 MADISON 8826.54 2691.61 4366.73 1768.2 661.47 313 729.03 1295.74 313 931.72 

2004 SUWANNEE 27980.11 13319.84 11903.25 2757.01 1342.75 891.8 2100.82 3750.73 892.3 3101.04 

2004 TAYLOR 701.52 115.2 470.72 115.6 68.2 29.05 67.53 87.09 29.59 70.36 

2004 UNION 9053.55 3405.1 5489.06 159.39 806.29 565.21 927.5 1565.38 565.83 1051.69 

 

2005 ALACHUA 18082.63 2795.18 12649.93 2637.52 1690.25 563.48 1422.96 2206.58 569.66 1777.69 

2005 BAKER 1530.88 336.58 1144.95 49.35 175.85 77.56 139.1 246.94 78.18 163.37 

2005 BRADFORD 2771.33 1219.36 1520.84 31.13 248.1 84.05 202.58 473.39 85.17 301.85 

2005 COLUMBIA 9497.09 1861.23 6819.45 816.41 1094.01 443.56 1002.58 1446.57 444.26 1151.86 

2005 DIXIE 8759.74 1271.49 2301.27 5186.97 323.34 147.48 342.93 497.77 158.69 407.98 

2005 GILCHRIST 20610.94 4273.11 13723.47 2614.36 1882.91 740.47 2340.73 3366.02 740.47 2641.17 

2005 HAMILTON 5450.49 1677.58 3764.71 8.2 310.54 338.43 623.34 648.84 397.58 711.3 

2005 JEFFERSON 7435.26 2172.84 5005.62 256.81 688.89 497.53 743.38 1278.28 497.67 780.21 

2005 LAFAYETTE 6053.96 2641.57 3344.74 67.65 435.97 240.07 633.31 930.26 240.07 896.16 

2005 LEVY 23687.33 3839.27 11887.86 7960.2 1698.93 769.24 2071.2 2589 772.97 2404.04 

2005 MADISON 8204.55 2066.4 4277.89 1860.26 659.1 320.6 786.24 1131.88 321.5 901.29 

2005 SUWANNEE 25867.33 11994.53 10551.05 3321.75 1411.57 808.77 1796.17 3772.08 809.07 2832.24 

2005 TAYLOR 1252.33 287.57 939 25.76 158.43 213.09 80.65 247.82 213.17 82.38 
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2005 UNION 4223.4 1309.95 2517.59 395.85 362.1 186.93 419.98 636.98 187.12 486.11 

 

2006 ALACHUA 26690.89 2380.67 19012.5 5297.72 2273.32 869.44 1290.08 2834.85 875.64 1542.56 

2006 BAKER 1523.73 132.74 1210.07 180.93 184.25 76.48 137.72 217.84 77.04 155.17 

2006 BRADFORD 6033.19 1176.21 4781.23 75.75 444.41 291.2 157.63 673.49 291.56 218 

2006 COLUMBIA 8679.22 2024.36 5994.51 660.35 928.35 329.45 852.94 1318.51 330.43 974.79 

2006 DIXIE 6545.11 563.92 2325.45 3655.74 395.11 139.08 297.14 527.89 148.81 372.27 

2006 GILCHRIST 23153.77 5069.94 13446.75 4637.09 1931.27 712.82 2271.41 3315.42 712.87 2516.76 

2006 HAMILTON 5177.98 1655.57 3376.3 146.11 319.63 250.88 574.45 665 276.31 693.93 

2006 JEFFERSON 9703.11 2712.46 6628.76 361.9 928.19 625.13 962.74 1706.6 627.63 966.87 

2006 LAFAYETTE 7635.1 3302.78 4009.49 322.83 526.52 244.32 509.02 1178.43 248.82 816.4 

2006 LEVY 18571.29 3094.4 11265.41 4211.49 1734.22 822.39 1788.4 2525.55 825.86 1889.42 

2006 MADISON 8076.46 2473.55 4394.75 1208.15 681 310.88 764.32 1267.1 314.21 874.4 

2006 SUWANNEE 26087.35 11577.03 10308.5 4201.83 1370.12 699.97 1682.52 3479.04 700.35 2955.42 

2006 TAYLOR 1288.06 685.18 514.26 88.62 87.66 31.82 76.22 227.63 32.26 79.2 

2006 UNION 3452.61 881.48 2563.13 8 415.72 223.07 388.6 568.96 223.07 451.45 

 

2007 ALACHUA 26835.87 3030.61 19313.11 4492.14 2106.85 769.28 1318.81 2734.95 778.41 1632.43 

2007 BAKER 990.48 67.93 815.29 107.26 130.12 47.49 70.23 151.59 49.03 71.63 

2007 BRADFORD 3002.41 1279.05 1588.55 134.81 253.9 86.33 84.03 487.09 88.03 152.82 

2007 COLUMBIA 9179.55 1855.47 6786.61 537.47 1125.35 337.5 842.07 1473.54 339.59 1064.34 

2007 DIXIE 6932.56 491.54 2461.86 3979.16 444.41 185.2 287.31 557.94 190.12 356.83 

2007 GILCHRIST 20475.53 5211.81 12295.62 2968.1 1780.44 623.87 1876.34 2949.91 624.31 2486.98 

2007 HAMILTON 5492.59 1882.87 3603.72 6 354.97 260.01 637.28 803.12 279.32 745.3 

2007 JEFFERSON 8746.09 2872.58 5773.35 100.16 783.26 610.07 834.87 1647.12 610.3 835.08 

2007 LAFAYETTE 7664.81 3488.3 3544.43 632.09 507.03 211.61 536.03 1207.52 216.12 827.66 

2007 LEVY 20243.06 4146.19 10457.86 5639.01 1590.59 513.31 1606.9 2508.4 530.88 1841.2 

2007 MADISON 9793.33 2988.41 4554.05 2250.87 788.8 234.8 724.45 1434.89 237.66 935.36 

2007 SUWANNEE 29372.26 13427.71 11410.64 4533.91 1442.51 810.61 1810.39 4057.13 811.8 3071.35 

2007 TAYLOR 647.2 214.84 366.19 66.17 58.48 20.93 47.18 121.02 21.8 50.48 

2007 UNION 7538.5 3144.28 4225.59 168.64 642.2 342.02 654.1 1388.36 342.06 817.12 
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Appendix D Public Comments 

Bureau of Onsite Sewage Programs 

Florida Department of Health

Please find a below a few comments on the in the draft Suwannee-TMDL, mainly related to the role of onsite 

sewage treatment and disposal systems discussed in the 

document(http://www.dep.state.fl.us/water/tmdl/docs/tmdls/draft/gp1/suwanneebasinnutrienttmdl.pdf).

 

p. 35 "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. "

Comment: The definition appears to only address rainfall-driven or stormwater sources. Consistent with this it only 

mentions failing septic systems as a potential source, which would be the only ones susceptible to stormwaterrunoff. With such a stormwater-centric definition how does this TMDL intend to address groundwater-driven 

sources of pollution, such as fertilizer or wastewater entering groundwater and eventually discharging from a 

spring? Groundwater contributions appear to be an important part in the Suwannee River Basin (e.g. in the cited 

Pittman et al. 1997 report)

 

p. 35 "Table 4.1 and figures 4.1-4.4 identify the facilities authorized for surface water discharges into the Suwannee 

River Basin. These point sources do not discharge into impaired waters or the main stems of the rivers. These point 

sources have an effect on the SRB on a planning unit wide basis. "

Comment: It is unclear why facilities are listed that discharge to non-impaired water bodies, but facilities that 

recharge to groundwater are not listed. Both could have an effect "on a planning unit wide basis". 

 

p.40 "At this time the Department is compiling nonpoint source data on historic row crop acreage and numbers of 

beef cattle, dairy cattle and poultry in the basin. These nonpoint sources will be address as the information becomes 

available. Appendix C has tables of historic to present fertilizer sales. Figure 4.4 depicts the onsite sewage locations 

in the SRB. The Department at this time has an incomplete record of septic tanks in the SRB and will be add this 

information as it updated. "

p. 41 "Figure 4.4 Onsite Sewage in the Suwannee River Basin"

 

Comment: What is the source for the shown data on number and location of OSTDS? Do the points represent all 

systems or only recently permitted ones? How many systems are estimated to be there?

 

Comment: It may be of interest to DEP's efforts in this watershed that an inventory of onsite systems in the 

floodplain of the Suwannee River was performed in the early 1990s for the Department of Health and Rehabilitative 

Services, in cooperation with the Suwannee River Water Management District. This inventory included an 

assessment of system functioning. This office has hard copies of several annual reports from this project.

 

Regards,

 

Eberhard Roeder

 

Eberhard Roeder, Ph.D., Prof. Eng. III 

Bureau of Onsite Sewage Programs 

Florida Department of Health 

4052 Bald Cypress Way, Bin# A-08 

Tallahassee FL 32399-1713
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In Response to Comments

Thank you for your comments they have been considered and the document has been edited where appropriate. The 

Suwannee river basin is a unique system the flows in lower portion of the river are dominated by groundwater. 

Groundwater contributions along with many other possible nonpoint sources were considered in this TMDL. 

Facilities that recharge to groundwater will need to be considered as possible sources. The document has been 

updated to reflect the source of the data (DOH 2007) and system estimates were included. Thank you for your 

comments and additional information.
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In Response to Comments 

Thank you for your comments they have been considered and the document has been edited where appropriate. 

Response to comment 1. It is unclear what level of reduction required by EPA you are referring to in this comment. 

EPA has not established pollutant reduction levels for the Suwannee and Santa Fe Rivers. Once the state adopts a 

TMDL pursuant to the Florida Watershed Restoration Act, the TMDL is submitted to EPA for their review and 

approval. EPA has responsibility to ensure that the TMDL is sufficient to restore the waterbody such that 

designated uses and their associated water quality standards will be met.

Response to comment 2. Based on 2004 land use Geographic Information System (GIS) coverages, roads and 

highways in the Suwannee and Santa Fe Rivers represent less than 1 percent of the acreage. However, as required 

by the Florida Watershed Restoration Act, pollutant load reduction allocations must be equitable and assure that all 

parties that contribute pollutants are part of the solution. There are certain very intensive land use activities that 

could represent a small percentage of a watershed yet contribute a significant fraction of a pollutant to receiving 

water

Response to comment 3. The data were used to designate the Suwannee and Santa Rivers as a Verified Impaired 

water in accordance with the procedures within Chapter 62-302, Florida Administrative Code (Impaired Waters 

Rule). This rule included requirements to assess data sufficiency, data quality, etc. 

Response to comment 4. . It is well known that stormwater from all land uses, including roads, contains nutrientts. 

Additionally, please remember that the stormwater within FDOT’s stormwater systems is not just from roads, but 

also from adjacent land uses. Accordingly, FDOT has an obligation to be a partner in reducing these pollutant 

loadings.

Response to comment 5. Differences in acres and total acre can be attributed to different methods of measurement 

and quantification of land use. This will be noted in the document.

Response to comment 6. As described in section 4.1, the source assessment section does not make a distinction 

between NPDES stormwater discharges and non NPDES stormwater discharges. The purpose of this section is to 

identify potential sources that might contribute the pollutant(s) of concern that need to be reduced to achieve 

designated uses and a more detailed evaluation of sources and allocation will be developed as part of the BMAP.

Response to comment 7. Pursuant to both Federal and state law and regulations, stormwater discharges are sources 

of pollution, are subject to regulation, and their pollutant loadings must be reduced once a TMDL is established. 

Development of the BMAP will focus approaches to achieve pollutant source reductions in an equitable and cost 

effective manner.

Response to comment 8. As discussed in the document, similar percent reductions were applied to the NPDES 

stormwater MS4s and the non NPDES stormwater discharges. A more detailed evaluation of sources and allocation 

will be developed as part of the BMAP. The BMAP process will also consider existing and proposed best 

management practices in the basin and approaches to achieve pollutant source reductions in an equitable and cost 

effective manner.

Response to comment 9. Section 6.1 describes how NPDES stormwater discharges are part of the WLA fraction of 

the TMDL while non NPDES stormwater discharges are represented by the LA. These categories are also reflected 

in the TMDL components of Table 6.1

Response to comment 10. Based on further analysis and discussion with stakeholders, the nitrate target is now 0.35 

mg/L and the document has a more detailed discussion on the development of the target.
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In Response to Comments 

Thank you for your comments they have been considered and the document was edited where appropriate.

Response to comment 1. The target is for nitrate as nitrogen (NO3-N). This has been clarified in the document.

Response to comment 2. The figure axis has been corrected.

Response to comment 3. The design flow has been corrected.

Response to comment 4. Additional information has been incorporated into the document regarding potential 

contributions of nitrogen from a variety of anthropogenic activities in the basin.

Response to comment 5. A weight of evidence approach was used to evaluate biological responses to nutrients. 

Resources and information necessary to link a ground water and surface model and incorporate biological responses 

were not available. A long-term monitoring program of paired nutrient and periphyton data provided site specific 

information to establish a nutrient target that was supported by other studies in Florida.
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Response to comment 6. The periphyton data set used to develop the nitrate target was based upon long-term stream 

monitoring sites in the Withlacoochee, Suwannee, and Santa Fe Rivers. Another line of evidence (Stevenson, 2007) 

included both field and laboratory measurements focused on springs and included eight springs in the Suwannee 

River Basin. Photographs included in the document include algal mats as well as algal blooms that have occurred in 

portion of the Suwannee and Santa Fe as well as springs over the past seven years.

Response to comment 7. Based upon the recommendation of Mr. Rob Matteson (previous aquatic biologist at the 

Suwannee River Water Management District (SRWMD), station SUW275 was excluded for the analysis due to 

possible marine influence.

Response to comment 8. As noted in the first comment there may have been some confusion in that the nitrate 

target was expressed as Nitrate-N rather than as nitrate. Based upon addition periphyton data provided by the 

SRWMD, the period was extended to 2007 and the revised target was changed from 0.286 mg/L to 0.35 mg/L 

nitrate-N.

Response to comment 9. Additional text will be added to the document.

Response to comment 10. The Department could not find a link between total phosphorus concentrations and 

imbalances in flora or fauna. The Department will continue to monitor and collect data to evaluate whether 

phosphorus adversely impacts aquatic flora or fauna as nitrate concentrations are reduced.

Response to comment 11. The TMDL identifies potential sources of nutrients to the system but detailed allocations

are developed as part of the basin management action plan (BMAP) process. The BMAP is a stakeholder consensus 

driven process with the goal of achieving the TMDL through development of allocations that are equitable and cost 

effective.. 
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In Response to Comments 

Thank you for your comments they have been considered and the document was edited where appropriate. 

Following the presentation to the Suwannee River Partnership (SRP) Executive Committee on May 30, 2008 as to 

the approach to establishing a TMDL target, staff have had numerous meetings with technical representatives from 
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the SRP to refine the analysis. As part of that process the Department has looked at the effects of flow, color, water 

temperature and Nitrate-N on cell density and biomass. Nitrate-N was found to still have significant correlation 

when held independent of the other parameters and was also the highest correlation. Through a collaborative 

process the available periphyton dataset was expanded to cover a 17 year period of record and the original target for 

Nitrate-N was modified from 0.286 mg/L to 0.35 mg/L. The goal of a TMDL to ensure that the designated uses are 

maintained. 

Part of the mission of the Suwannee River Partnership formed in 1999 was to reduce nitrate levels in the surface 

waters and ground water within the Suwannee River basin. Components of the SRP include research, evaluation of 

best management practices (BMPs), public education and outreach, and funding support for implementation of 

BMPs. With more than 60 Federal, State, and Local agencies as well as private associations and businesses the 

basin management action plan process will build upon the SRP. 
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Gilchrist Soil and Water Conservation District 

P.O. Box 37 – Bronson, Florida 32621 – Phone (352) 

July 18, 2008 

Andrew Bartlett 

Department of Environmental Protection 

Dear Mr. Bartlett, 

The Gilchrist Soil & Water Conservation District (GSWCD) is sending this letter regarding the Total Maximum 

Daily Load (TMDL) set at 0.286 mg/L for the Middle/Lower Suwannee River and the Lower Santa Fe River as 

presented in the meeting on July 10, 2008 by the Florida Department of Environmental Protection (FDEP). GSWCD 

board supervisors felt that the data presented during the meeting was insufficient in quality and quantity to set a limit 

that has such magnitude and far reaching implications for the residents, farmers, industry, and governmental 

agencies in the Suwannee Basin. 

The GSWCD would like to request that FDEP consider the water quality and biological data made available by the 

Suwannee River Water Management District to develop a more appropriate TMDL limit. As comments at the 

Chiefland meeting suggested a more holistic approach would be a better form of evaluation for such a complex 

riverine system. As a representative of the county it is the responsibility of GSWCD to oversee and assist 

conservation practices in Gilchrist County and we believe that a sound scientific approach should be used for the 

TMDL development process. 

 

The Gilchrist Soil and Water Conservation Board’s mission is to deliver natural resources conservation technology 

and education to local land users and to promote the best land use and management practices that will conserve, 

improve and sustain the natural environment of Gilchrist County. Once a TMDL is established using sound science 

the GSWCD would like to be involved in the basin management action plan (BMAP) development process as we 

have first hand knowledge of the resources in Gilchrist County. Thank you for your consideration in this critical 

matter. 

Sincerely, 

Kelly Philman, Chairman 

Gilchrist Soil & Water Conservation District 

CONSERVATION – DEVELOPMENT – SELF GOVERNMENT 

In Response to Comments 

Thank you for your comments they have been considered and the document was edited where appropriate. As 

discussed at the July 10, 2008 public meeting, additional information provided by the Suwannee River Water 

Management District was incorporated into the analysis to establish the nitrate target. The revised analysis includes 

data from 1999-2007 for total of 17 years and as a result the target has been amended to 0.35 mg/L. The goal of a 

TMDL to protect any critical condition that may occur. Terry Hansen [terry.hansen@dep.state.fl.us, (850) 245-

8561] is the Department’s basin coordinator who will be facilitating the basin management action plan (BMAP) 

process. The BMAP process is a stakeholder consensus driven process that focuses on approaches to achieve 

pollutant source reductions in an equitable and cost effective manner. 
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From: Merrilleeart@aol.com [mailto:Merrilleeart@aol.com] 

Sent: Tuesday, September 23, 2008 10:56 PM 

To: Bartlett, Drew 

Subject: Thursdays Meetings questions and comments from audience member

Hello Drew, 

I was the sole member of the audience from the outside at the TMDL hearing last week. As per your 

request to e-mail my questions and comments...here they are. 

 

1. Why was the figure .286 changed to .35 for allowable nitrates? 

 

2. The Suwannee River and the Santa Fe River are two distinct river bodies and need to be separated 

while doing these kind of studies. 

 

3. What is the situation with the Vaucheria on the Suwannee River? 

 

Terry and Constance were very helpful after the meeting to answer any of my questions and offer me 

feedback on the TMDL Study. 

 

I realize the magnitude of issuing compliance now that these levels have been set. I offer my service of 

including any public information to my weekly e-mail list to help get the word out on anything pertaining to 

protecting our waterways. 

 

Thank You, 

Merrillee Malwitz-Jipson 

board member Our Santa Fe River, Inc. 

High Springs, FL 

Merrilleeart@aol.com

www.oursantaferiver.org

In Response to comments

Thank you for you comments.

Response to comment 1. The initial draft TMDL report included periphyton data from 1990 to 1998. Since the 

initial draft report additional information provided by the Suwannee River Water Management District was 

incorporated into the analysis to establish the nitrate target. The revised analysis includes data from 1999-2007 for a 

total of 17 years. The same analysis was performed on the expanded data set and provided greater statistical 

confidence on the exponential regression used in the target setting. The expanded data set, updated analysis, and 

greater statistical confidence provided the Department with assurance that the current target (0.35 mg/L nitrate) will 

protect the waterbody and prevent future excessive algal growth. For further explanation of the target setting please 

refer to section 5.5 in this report.

Response to comment 2. The Suwannee and Santa Rivers are different basins but with similar characteristics, such 

as land use land, karst terrain and both are dominated by groundwater inputs in their lower portions. Also both river 

systems have shown remarkably similar water quality trends through out the period of record. The Periphyton data 

set used to set the TMDL encompassed Suwannee River, Santa Fe River, and Withlacoochee River sampling 

locations. The TMDL report is written for both Suwannee and Santa Fe River Basins but the TMDL itself is 

separate for both basins and the percent reductions are calculated by basin. 

Response to comment 3. The Suwannee River was listed as impaired based on photographic evidence of algal mats. 

Vaucheria spp. is a common taxa of macroalgae that occurred in extensive growths and was studied in several of the 

lines of evidence in this TMDL report. For more information on Vaucheria spp. in spring sampling please contact 

Connie Bersok (Connie.Bersok@dep.state.fl.us, (850) 245-8479).
TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River 

Page 117 of 117 

Florida Department of Environmental Protection 

9/24/2008 

Florida Department of Environmental Protection 

Division of Water Resource Management 

Bureau of Watershed Management 

2600 Blair Stone Road, Mail Station 3565 

Tallahassee, Florida 32399-2400 

(850) 245-8561 

www2.dep.state.fl.us/water/