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 (3 422R), 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

9/24/08TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 2 of 117 Florida Department of Environmental Protection 9/24/2008 

# Acknowledgments

The development of this Total Maximum Daily Load (T MDL) 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 th e 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 assistan ce by Latrincy Whitehurst, as Latrin cy 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) 245-8356TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 3 of 117 Florida Department of Environmental Protection 9/24/2008 

# Contents

Nutrient and Dissolved Oxygen TMDL for th e 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 Rive r Basin...........................................................................................................

.................. 8 1.2.2 Santa Fe Ri ver Basin ...........................................................................................................

.................. 14 1.3 Background .................................................................................................................

......................................... 16 

### Chapter 2: DESCRIPTION OF WATER QUALITY PROBLEM ......................................... 18
2.1 Statutory Requirements an d Rulemaking History ..................................................................................

.. 18
2.2 Information on Veri fied 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 Classificati on (OFW)................................................................................

... 34
3.4 Watershed Management Basi n Rotation Cycle 1 ....................................................................................

.. 34
3.5 Suwannee River Partnership and Reas onable Assurance Documentation ............................................. 34 

### Chapter 4: ASSESSMENT OF SOURCES............................................................................. 35
4.1 Types of Sources ...............................................................................................................

............................ 35
4.2 Point Sources in the Suwannee Rive r 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......................................................................................................................

.................... 48TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 4 of 117 Florida Department of Environmental Protection 9/24/2008 

### Chapter 5: DETERMINATION OF ASSIMILATIVE CAPACITY ...................................... 55
5.1 Hydrology......................................................................................................................

................................ 55
5.2 Water Qualit y Over Time........................................................................................................

.................... 57
5.3 Flows over time................................................................................................................

............................. 59
5.4 Biological Effects .............................................................................................................

............................. 60
5.5 Nitrate (NO 3 ) Target .......................................................................................................................

............. 60 5.5.1 Laboratory nutrient amendment bioassays ........................................................................................ 60 5.5.2 Relationship between ecological effici ency 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 periphyt on biomass and cell density an d nitrate conc entration...................... 62 5.5.5 Target Settin g. ................................................................................................................

................... 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 A llocati on........................................................................................................... ......................... 75 6.3.1 National Pollutant Discharge Elimina tion System Stormw ater Discharges .......................................... 75
6.4 Margin of Safety ...............................................................................................................

............................ 75
6.5 Recommendations for Further Studies............................................................................................

........... 76 

### Chapter 7: NEXT STEPS: IMPLEME NTATION 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 th e Suwannee River Algal Data.............................. 81 Appendix C Historic Fertil izer 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 an d 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 ma jor cities in study area......................................................................... 15 Figure 2.1 Middle Suwann ee WBIDs ..........................................................................................................

............ 21 Figure 2.2 Lower Suwann ee WBIDs ...........................................................................................................

............ 22 Figure 2.3 Santa Fe WBIDs .................................................................................................................

................... 23 Figure 2.4 Total Phosphorus-Three Year Ro lling Average by Planning Unit ........................................................ 25TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 5 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 2.5 Rolling Average TP concentrations for the Middle Suwannee River and TP fertilizer sales for Suwannee and Lafa yette co unties................................................................................................

................................ 25 Figure 2.6 Middle Suwannee Aerial and Sampling Statio n Locations .................................................................... 28 Figure 2.7 Lower Suwannee Aerial and Sampling Statio n Locations ..................................................................... 29 Figure 2.8 Santa Fe Aerial and Sa mpling Statio n Locations .................................................................................

. 30 Figure 2.9 Photographic evidence 2000 .....................................................................................................

............ 31 Figure 2.10 Additional Photogr aphic 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 th e Santa Fe Ri ver Ba sin..............................................................................

.. 39 Figure 4.4 Total Nitrogen inputs in the Middl e 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 Basi n Populati on Density .......................................................................................

.. 45 Figure 4.10 Santa Fe Basin P opulation Density..............................................................................................

..... 46 Figure 4.11 Principal land uses in the drainage basin of the Middl e Suwannee River. ....................................... 49 Figure 4.12 Principal land uses in the drainage basin of the Middl e Suwannee River. ....................................... 50 Figure 4.13 Principal land uses in the drainage basin of the Lowe r Suwannee River. ........................................ 51 Figure 4.14 Principal land uses in the drainage basin of the Lowe r Suwannee River. ........................................ 52 Figure 4.15 Principal land uses in the draina ge basin of the Santa Fe River. ..................................................... 53 Figure 4.16 Principal land uses in the draina ge 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 Sant a 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 effic iency 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 St udy Sites.......................................................................................................

................ 63 Figure 5.9 Relationship between mean nitrate concentration and mean periphyton biomass from 12 sampling sites on the Suwannee, Santa Fe, and Withlac oochee Rivers ......................................................................

................ 64 Figure 5.10 Relationship between mean nitrate concentration and mean periphyton cell density from 12 sampling sites on the Suwannee, San ta Fe, and Withla coochee Rivers.............................................................

.......... 65 Figure 5.11 Change Point Analyses the 95% confidence interval ........................................................................ 66 Figure 5.12 Central Tendency and Upper 95% Confidence interv al approach ................................................... 67 Figure 5.13 Upper and Lower 95% Confiden ce Interval approach. .................................................................... 68 

# List of Tables

Table 1.1 WBIDs in the Middle Su wannee Planni ng Unit..................................................................................... 12 Table 1.2 WBIDs in Lower Suw annee Planni ng Unit..........................................................................................

.. 14 Table 1.3 WBIDs in the Santa Fe Plannin g Unit............................................................................................

....... 15 Table 2.1 Cycle 2 Verified List fo r Suwannee River Basin .................................................................................

... 18 Table 2.2 Summary of DO Data by Month for the Verifie d Period (June 1, 2000 – June 30, 2007)..................... 26 Table 2.3 Summary of DO Data by Season for the Ver ified Period (June 1, 2000 – June 30, 2007).................... 26 Table 2.4 Summary of DO Data by Year for the Verifi ed Period (June 1, 200 0 – June 30 , 2007)........................ 27 Table 4.1 NPDES permitted facilities identified in the drain age basin discharge to Suwannee River Basin........ 35 Table 4.2 MS4 Perm ittees

................................................................................................................. ..................... 40 Table 4.3 Estimated Number of Onsite Sewage Treatm ent Systems ...................................................................... 42 Table 4.4 Population and number of household in SRB ......................................................................................

.. 43 Table 4.5 Animal Operations 2007 Es timates by pl anning unit ............................................................................ 47TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 6 of 117 Florida Department of Environmental Protection 9/24/2008 Table 4.6 Total Nitrogen cont ribution es timates. .........................................................................................

......... 47 Table 4.7 Acreages and percent acreages of differe nt land use catego ries for the SRB........................................ 48 Table 5.1 Spearman Correlation on Ce ll Density an d Biomass ............................................................................ 69 Table 5.2 Multiple Regression on Ce ll Density an d Biomass................................................................................ 69 Table 5.3 Partial correlation on Ce ll density and biomass ................................................................................

... 70 Table 5.4 NO 3 + NO 2 Concentrations (mg/L) in the Main Stem WBIDs over the 1999 - 2006 period, Middle Suwannee River .................................................................................................................

.......................................... 71 Table 5.5 NO 3 + NO 2 Concentrations (mg/L) in the Main Stem WBIDs over the 1999 - 2006 period, Lower Suwannee River .................................................................................................................

.......................................... 71 Table 5.6 NO 3 + NO 2 Concentrations (mg/L) in the Main Stem WBIDs over the 1999 - 2006 period, Lower Santa Fe River 71 Table 5.7 Median NO 3 in Springs w ithin 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 n itrate concentration (mg/L) ....................................................................... 75 Table C.1 Historic Total Nitrogen Sales 1945-199 1 (Tons).................................................................................

.. 95 Table C.2 Historic Total Phosphorus Sales 1945-1991 (Tons).............................................................................. 96 Table C.3 1998 to 2007 Fertiliz er Sales (Tons) ...........................................................................................

.......... 97TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 7 of 117 Florida Department of Environmental Protection 9/24/2008 

# 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/wat er/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 Adviso ry 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/TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 8 of 117 Florida Department of Environmental Protection 9/24/2008 

# Chapter 1: INTRODUCTION

1.1 Purpose of Report
This document presents Total Maximum Daily Loads (TMDLs) for Nitrate (NO 3 ) 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 us ed 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 in clude 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 approximatel y 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 wate rsheds lie almost entirely in Geor gia. 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 str eams typically have low dissolved oxygen (DO) concentrations and acidic, highly colored water and these streams ar e 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 r echarge 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, sh allow water, and fresh water inflows. Seagrass beds are healthy and abundant, except at the mouths of the river wher e 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 alon g 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 ecologi cal 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 Cal careous Reach 6. EstuarineTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 9 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 1.1 Suwannee Santa Fe ReachesTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 10 of 117 Florida Department of Environmental Protection 9/24/2008 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 ri ver 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
w ater b ody id entification (WBID) number for each wa tershed or stream reach. The main stem of the SRB is divided into fifteen segments. WBIDs are combined into larger un its called Planning Units. Figures 1.2-1.4 illustrate the Middle Suwannee, Lower Suwannee and Santa Fe Planning Un its and Tables 1.1-1.3 list the WBIDs in each of the Planning Units.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 11 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 1.2 Middle Suwannee Planning Unit and major cities in study areaTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 12 of 117 Florida Department of Environmental Protection 9/24/2008 Table 1.1 WBIDs in the Mi ddle 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 DitchTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 13 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 1.3 Lower Suwannee Planning Unit and major cities in study area.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 14 of 117 Florida Department of Environmental Protection 9/24/2008 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 spri ng-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, ex cept for the Santa Fe and Ichetucknee Rivers and Cow Creek. The upper watershed is characterized by nearly le vel pine flatwoods with gently rolling h ills. Tributary streams are fairly well incised into the landscape, which occasionally opens into br oad, 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).TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 15 of 117 Florida Department of Environmental Protection 9/24/2008 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 DrainTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 16 of 117 Florida Department of Environmental Protection 9/24/2008 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 rota tes 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 assim ilate and still meet water quality standards, including its applicable water quality criteria and its designated uses. TMDLs are developed forTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 17 of 117 Florida Department of Environmental Protection 9/24/2008 waterbodies that are verified as not meeting their wate r 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 act ive participation of the SJRWMD, local governments, businesses, and other stakeholders. The Department will wo rk 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

Page 18 of 117 Florida Department of Environmental Protection 9/24/2008 

# Chapter 2: DESCRIPTION OF WATER QUALITY PROBLEM

2.1 Statutory Requirements and Rulemaking History
Section 303(d) of the Clean Water Act re quires states to submit to the EPA a lis t 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 ba sin is also required by the FWRA (Subsection 403.067[4)] Florida Statutes [F.S.]), and the list is amended a nnually 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, Flor ida 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 veri fied 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, 2 008. Figures 2.1-2.3 show a ll the WBIDs located in the Middle Suwannee, Lower Suwannee, and Sa nta Fe Planning Units, respectively.
Table 2.1 Cycle 2 Verified Li st 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 Stre am 2 Fecal Coliform Low
Lower Suwannee 3733 Direct Runoff To Gulf Stream 2 Fecal Coliform (3) LowTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 19 of 117 Florida Department of Environmental Protection 9/24/2008 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 Co liforms 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 MediumTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 20 of 117 Florida Department of Environmental Protection 9/24/2008 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 HighTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 21 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 2.1 Middle Suwannee WBIDsTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 22 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 2.2 Lower Suwannee WBIDs

.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 23 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 2.3 Santa Fe WBIDsTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 24 of 117 Florida Department of Environmental Protection 9/24/2008 

### 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 NO 3 as nitrogen (NO 3 N) and for the purposes of this repo rt, unless otherwise stated, the sum of NO 3 and nitrite (NO 2 ) is used to represent NO 3 due to minimal contributions of NO 2 . Chapter 5 discusses the nitrate (NO 3 ) nutrient impairment and the setting of the target concentration of NO 3 . 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, whic h 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 surroundi ng 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 purp oses of this TMDL the Department could not link the impairments with either phosphorus load or c oncentration and, therefor e, will be targeting NO 3 to achieve standards. Monitoring and evaluation for total phosphorus should continue as this TMDL is implemented.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 25 of 117 Florida Department of Environmental Protection 9/24/2008 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 YEARTOTAL 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 YearTP (Tons)



### 0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45TP (mg/L) TP (Tons) Rollinng average TPTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 26 of 117 Florida Department of Environmental Protection 9/24/2008 

### 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 th e 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% 3605ATMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 27 of 117 Florida Department of Environmental Protection 9/24/2008 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% 3605CTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 28 of 117 Florida Department of Environmental Protection 9/24/2008 

### 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 LocationsTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 29 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 2.7 Lower Suwannee Aerial and Sampling Station LocationsTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 30 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 2.8 Santa Fe Aerial and Sampling Station LocationsTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 31 of 117 Florida Department of Environmental Protection 9/24/2008 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 resu lt in increased algal abundance.” In the years prior to the report there were flow events that led to extensive gr owth 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 2000TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 32 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 2.10 Additional Photographic Evidence.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 33 of 117 Florida Department of Environmental Protection 9/24/2008 

# Chapter 3: DESCRIPTION OF APPLICABLE WATER QUALITY STANDARDS

3.1 Classification of the Waterbody a nd 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 cu rrently in this class)

Both the Suwannee River and Santa Fe River are Class II I waterbodies, with a desi gnated 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. N ormal 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 fl ora or fauna. Accordingly, a nutrient-related target was needed to represent levels above which an imbalance in flora or fauna is exp ected to occur. A threshold commonly used for assessing the nutrient impairment in streams is the an nual average chl a concentration of 20 μ g/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, d ecrease in the distribution (either in de nsity or areal coverage) of seagrasses or other submerged aquatic vegetation, changes in algal species richness, and excessive diel oxygen swings.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 34 of 117 Florida Department of Environmental Protection 9/24/2008 

### 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, es tuarine research reserves, certa in waters within state or national forests, scenic and wild rivers, or aquatic pres erves. The Suwannee River and Santa Fe Rivers are both designated “Special Waters” because of their ex ceptional ecological and r ecreational significance.
The Suwannee River was designated an OFW in 1979. That year (pre-OFW) the annual NO 3 -N load was 3,548,981 kg N yr -1 and in 2005(post-OFW) the annual NO 3 -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, wate r 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 undert aken 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 Re asonable 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 pl an 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, fede ral and regional agencies, local governments and private industry representatives that had been formed in 1999 to reduce nitrate levels in th e 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 EP A 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 Partnershi p’s RA documentation. The EPA sited that “similar commitments have not been initiated in the Upper Suwa nnee 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 Manage ment District area.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 35 of 117 Florida Department of Environmental Protection 9/24/2008 

# Chapter 4: ASSESSMENT OF SOURCES

4.1 Types of Sources
An important part of the TMDL analysis is the identificati on of pollutant source categorie s, 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. So urces 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 wa stewater treatment facilities (WWTFs) are examples of traditional point sources. In contrast, the term “nonpoint sources” was used to describe intermittent, rainfall-drive n, 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 in dustrial 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 disc harges, 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 e ither 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 drai nage 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 AlachuaTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 36 of 117 Florida Department of Environmental Protection 9/24/2008 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 StormwaterTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 37 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 4.1 Wastewater Facilities in the Middle Suwannee River Basin.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 38 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 4.2 Wastewater Facilities in the Lower Suwannee River Basin.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 39 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 4.3 Wastewater Facilities in the Santa Fe River Basin.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 40 of 117 Florida Department of Environmental Protection 9/24/2008 4.2.1 Municipal Separate St orm 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 Phas e 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 lbsTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 41 of 117 Florida Department of Environmental Protection 9/24/2008 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 lbsTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 42 of 117 Florida Department of Environmental Protection 9/24/2008 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 we re 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 On site Sewage Treatment Systems

Planning Unit Number of Sites* Middle Suwannee 4,894 Lower Suwannee 4,630 Santa Fe 11,684 *Number of onsite sewage treatme nt 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 BasinTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 43 of 117 Florida Department of Environmental Protection 9/24/2008 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 2.56TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 44 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 4.8 Middle Suwannee Basin Population DensityTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 45 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 4.9 Lower Suwannee Basin Population DensityTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 46 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 4.10 Santa Fe Basin Population Density.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 47 of 117 Florida Department of Environmental Protection 9/24/2008 4.3.3 Animal Operations Table 4.5 shows the estimated population sizes of animal oper ations 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) C o n v e r s i o n * M e a n w t 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 3TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 48 of 117 Florida Department of Environmental Protection 9/24/2008 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, ap proximately 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 904,308 914,611 885,791TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 49 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 4.11 Principal land uses in the drainage basin of the Middle Suwannee River.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 50 of 117 Florida Department of Environmental Protection 9/24/2008 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 500000Urban and Built upAgricultureRangelandUpland ForestWaterWetlandBarren LandTransportation,Communication &UtilitiesAcres 1988 1995 2004TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 51 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 4.13 Principal land uses in the drainage basin of the Lower Suwannee River.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 52 of 117 Florida Department of Environmental Protection 9/24/2008 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 200000Urban and Built upAgricultureRangelandUpland ForestWaterWetlandBarren LandTransportation,Communication &UtilitiesAcres 1988 1995 2004TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 53 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 4.15 Principal land uses in the drainage basin of the Santa Fe River.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 54 of 117 Florida Department of Environmental Protection 9/24/2008 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 500000Urban and Built upAgricultureRangelandUpland ForestWaterWetlandBarren LandTransportation,Communication &UtilitiesAcres 1988 1995 2004TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 55 of 117 Florida Department of Environmental Protection 9/24/2008 

# 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 gro und water inflow to the river stemming from increases in anthropogenic activities. “Agricultural activities (croplan d farming, animal farming operations (beef and dairy cattle, poultry, and swine), along with atmospheric depos ition, 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.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 56 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 5.1 Floridian AquiferTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 57 of 117 Florida Department of Environmental Protection 9/24/2008 

### 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 NO 3 concentrations and loadings since the OFW designation of the Suwannee River in 1979.
On the Suwannee River, the area where th e largest increase in nitrat e concentration occurs is a 38 mile segment of the Middle Suwannee River Basin from Dowling Park to Br anford. In the Santa Fe River the largest increase is from US 441 to State Road 47 (Hornsby 2007). The monitori ng 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 NO 3 (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 YearNO3(mg/L) Rolling Average NitrateOFWDesignationTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 58 of 117 Florida Department of Environmental Protection 9/24/2008 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 YearNO3(mg/L) Rolling Average NitrateOFWDesignationTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 59 of 117 Florida Department of Environmental Protection 9/24/2008 

### 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 cumula tive 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 1972-2007TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 60 of 117 Florida Department of Environmental Protection 9/24/2008 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 i ndicates 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 YearNitrate Load (kg N/yr)

0 2,000 4,000 6,000 8,000 10,000 12,000 14,000 16,000 18,000Mean 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 Suwa nnee 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 nutri ent availability.” This same study also found that the most widely limiting nutrient was nitrogen. 

### 5.5 Nitrate (NO 3 

### ) 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) comp aring metabolic rates, specifically, ecological efficiency, of aquatic communities, 3) examin ing 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 nutrie nt 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 C ounty, Florida to achieve a reduction of biomass of Lyngbya wollei

. L. wollei is a nuisance blue-green benthic algal species that dominates the Rainbo w River due to elevatedTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 61 of 117 Florida Department of Environmental Protection 9/24/2008 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 ex periments, 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 nitr ate 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 no t 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 nu trient 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 effi ciency, 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-lev el property that estimates the overall efficiency of an aquatic ecosystem to utilize incident solar radiation. Figure 5.6 shows the correlation between the ecologi cal efficiency and nitrate concentration.
Figure 5.6 Correlation between ecological efficiency an d nitrate concentration in WR, RSR, ASC, and JC.

The target ecological efficiency defined using this method is 0.25 g O 2 /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 nu trient 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 withTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 62 of 117 Florida Department of Environmental Protection 9/24/2008 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 Ma dison Blue, Lafayette Blue, Troy, Little River, Turtle, Guranato, Fanning, and Manatee Springs (Figure 5.7).
Figure 5.7 Springs includ ed 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 n itrate 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 av erage 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).TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 63 of 117 Florida Department of Environmental Protection 9/24/2008 Figure 5.8 Change Point Study Sites

To further define the nitrate concentration that may signifi cantly 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 cri tical 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 goo dness-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 stepTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 64 of 117 Florida Department of Environmental Protection 9/24/2008 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 NO x 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 RiversTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 65 of 117 Florida Department of Environmental Protection 9/24/2008 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/cm 2 (P = 0.00), and the other is about 218,732 + 427,894 = 646,626 cells/cm 2 (P = 0.0001). In this study, the 218,732 cells/cm 2 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/cm 2 to 646,626 cells/cm 2 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/m 2 (P= 0.00), and the other level is about 1.82+2.97 = 4.79 g/m 2 (P = 0.00). In this study, the 1.82 g/m 2 was considered as the baseline condition under which no significant nitrate impact wa s detected. The nitrate concentration that significantly changed the biomass level from 1.81 g/m 2 to 4.79 g/m 2 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 th at allowed the biomass baseline condition was 0.441 mg/L.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 66 of 117 Florida Department of Environmental Protection 9/24/2008 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, n itrate was primary factor causing elevat ed 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, respectivel y. 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 NO 3 was 0.441 mg/L with the test statistic of 7.68 and confidence level over 95%. The 95% conf idence interval for the change point was between 0.378 mg/L and 0.629 mg/L of NO 3 (Figure 5.11), the lower bound being 0.378 mg/L NO 3 . It is important to note that the change point analysis provides a concentration of n itrate for which change occu rs. 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 NO 3 , 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 conclusi on 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 targ et was using the change point of 0.441 mg/L to identify an equivalent cell density conc entration relative to the central tendency (an exponential curve R 2 =0.72) of the relationship. Once identified, the nitr ate concentration prior to the change point can be identified by finding the equivalent Upper 95% Confidence Interval, i.e., a NO 3 value of 0.38 mg/L.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 67 of 117 Florida Department of Environmental Protection 9/24/2008 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% conf ident that the relationship holds. By taking the lower cell density at the change point of 0.441 mg/L, we have targeted a more co nservative condition in the wate rbody. 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 (F igure 5.13), i.e., a NO 3 value of 0.33 mg/L.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 68 of 117 Florida Department of Environmental Protection 9/24/2008 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 protec tive of the aquatic flora or fa una 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.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 69 of 117 Florida Department of Environmental Protection 9/24/2008 

### 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 nitrat e, algal cell density, algal biomass, and other water quality parameters collected in conjunction with periphyton. Nitr ate 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 va riables. Again nitrate’s co rrelations 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 NO 3 NO 2 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 NO 3 NO 2 + Color 0.622 0 0.528 0 Flow + Temperature 0.513 0 0.283 0.003 NO 3 NO 2 + Temperature 0.626 0 0.508 0 NO 3 NO 2 + Flow 0.64 0 0.492 0 Flow + Color + Temperature 0.554 0 0.32 0.004 Color + Temperature + NO 3 NO 2 0.627 0 0.57 0TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 70 of 117 Florida Department of Environmental Protection 9/24/2008 Flow + Color + Temperature + NO 3 NO 2 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 Nitr ate 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 NO 3 NO 2 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 NH 4 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).TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 71 of 117 Florida Department of Environmental Protection 9/24/2008 Table 5.4 NO 3 + NO 2 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 NO 3 + NO 2 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 NO 3 + NO 2 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 th is TMDL report and that the nitrate target should also be achieved in each of those WBIDs as well. The amount of nitr ate data collected in each spring vent is not adequate toTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 72 of 117 Florida Department of Environmental Protection 9/24/2008 calculate a monthly average. However, for informati on 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 NO 3 in Springs within the SRB

WBID Name Median NO 3 (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%TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

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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 allo cating acceptable loads among all of the known pollutant sources in a watershed so that appropriate control m easures can be implemented and water quality standards achieved. A TMDL is expressed as the sum of all point source loads (wasteload alloca tions, 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 betw een 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 ≅ ∑

 WLAs wastewater + ∑

 WLAs NPDES 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 reduc tion, 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 disc harges cannot be centrally collected, monitored, and treated, they are not subject to the same ty pes 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 NO 3 (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 ).TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 74 of 117 Florida Department of Environmental Protection 9/24/2008 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 WLA NPDES wastewater WLA NPDES 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 reduc tion calculation. If the overall TMDL (0.35 mg/L) is the basi s for the percent reduction and the percent reduction may be differen t 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 redu ctions are the expression of the TMDL that will be implemented, EPA 1 recommends that all TMDLs and associated load allocations and wasteload allocations include a daily time increment in conjunction with other approp riate temporal expressions that may be necessary to implement the relevant water quality standard. Daily maximum concentration target for nitrate was established using the following equation 2 , which assumes that the nitrate data di stributions are lognorm al in Suwannee and Santa Fe River Basins:
MDL = LTA * exp(Z p σ y – 0.5 σ y 2 )

σ y

= sqrt(ln(CV 2 + 1))

Where
LTA = long-term average (0.35 mg/L) Z p = pth percentage point of the standard normal distribution, at 95% (Z p =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, as suming 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 maxi mum nitrate target for the Suwannee and Santa Fe River Basins (Table 6.2)

. The means, STDEVs, and CVs of nitrate concentrat ions of different water segments are listed in Table 6.2.

1 November 2006 U. S. Environmental Protection Agency (USEPA 2006) Memorandum “Establi shing 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 Im plications for NPDES permits.” 2 EPA, “Options for Expressing Daily Lo ad in TMDL (The Option),” June, 2007.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 75 of 117 Florida Department of Environmental Protection 9/24/2008 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 target s were developed for illustrative purposes. Implementation of the TMDL will be based on the m onthly average concentration targets.


### 6.2 Load Allocation
Because no target loads were explicitly cal culated in this TMDL report due to th e lack of flow data at the outlet of each stream segment, TMDLs are represented as the percen t reduction required to achiev e the nitrate target. The percent reduction assigned to all the nonpoint sources ar eas (LA) are the same as those defined for the TMDL percent reduction. To achieve the annu al 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. Th e 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 Elimin ation 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 NP DES 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 sa me percent nitrate reduction re quired 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 respon sible 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 Allocatio n Technical Advisory Committ ee (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, th e nitrate target was established based on th e 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 c oncentration during the summer algal growth season based on seasonal analysis on the nitrate concentration, and theref ore adds to the margin of safety. In addition, when estimating the required percent reduction to achieve the wa ter quality target, the highest long-term monthly averages of measured nitrate concentrations, in stead of average long-term monthly aver ages, 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.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

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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 comp lex 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.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 77 of 117 Florida Department of Environmental Protection 9/24/2008 

# 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 do cument will be developed over the next two years in cooperation with local stakeholders, wh o 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 so urce identification n eeded in order to achieve the TMDL,

• Timetables for implementation,

• Confirmed and potential funding mechanisms,

• Any applicable sign ed agreement(s),

• Local ordinances defining actions to be taken or prohibited,

• Any applicable local water quality standard s, 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 w ill 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 re presents 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 esta blishment of this TMDL. The Partnership will play a significant role the Basin Management Action Plan process.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

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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, Sp atial 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. Grow th 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 Rehabilit ative Services (HRS), State of Fl orida 1993. Suwannee River Floodplain Onsite Sewage Disposal Systems Inventory, Annual Report 1993
Department of Health and Rehabilit ative Services (HRS), State of Fl orida 1994. Suwannee River Floodplain Onsite Sewage Disposal Systems Inventory, Final Report 1994
Florida Administrative Code. Chapter 62-302, Surface wat er 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 Wat er 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/environmen t/programs/ehgis/Eh GisDownload.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. Evalua tion of alternative stormwat er regulations for southwest Florida. Submitted to: Water Enhancement & Restorat ion Coalition, Inc. P repared 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 Manageme nt District, LiveOak, FL.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 79 of 117 Florida Department of Environmental Protection 9/24/2008 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 Wa ter Management District Technical Report WR-00-04. iv, 148 pp.
Hornsby, D. 2007. In fluences On The Distribution And Occu rrence Of Nitrate-Nitrogen And Total Phosphorus In The Water Resources Of The Suwanne e 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 ba sin, Florida. U.S. Geological Survey, Water Resources Investigations Repo rt, 99-4252. Ta llahassee, 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 Flor ida Department of Environmental Protectcion. St. Johns River Water Management District, Palatka, FL.
Oaksford, E.T., 1994, National Water-Quality Assessm ent 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. 1 997. 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 Environmenta l Protection, Tallahassee, FL. 58pp.
United States Census Bureau. Census 2007, Available at http://www.census.gov/
United States Department of Agriculture, National Agri culture Statistics Service, USDA 2007. Available at http://www.nass.usda.gov/Statistics_by_State/Florid a/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. Ci rcuit 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 administrato r, 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.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

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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 implem ent 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 Ch apter 403, F.S., was establis hed as a technology-based program that relies on the implementation of BMPs that ar e 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 floo d 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 di stricts 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 pa rt 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. Th ese stormwater discharges include cert ain 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 impl emented 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 NP DES 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 ca nnot be easily collected and treated by a central treatment facility, as are other point sources of pollution such as dome stic 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.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

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# Appendix B Change Point Analysis of the Suwannee River Algal DataTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

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Page 95 of 117 Florida Department of Environmental Protection 9/24/2008 

# Appendix C Historic Fertilizer Sales

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

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 731TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 96 of 117 Florida Department of Environmental Protection 9/24/2008 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) CountyYearAlachuaBakerBradfordColumbiaDixieGilchristHamiltonJeffersonLafayetteLevyMadisonSuwanneeTaylorUnion

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 115TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 97 of 117 Florida Department of Environmental Protection 9/24/2008 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 675TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 98 of 117 Florida Department of Environmental Protection 9/24/2008 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 2,847.64TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 99 of 117 Florida Department of Environmental Protection 9/24/2008 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 82.38TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 100 of 117 Florida Department of Environmental Protection 9/24/2008 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 1388.36 342.06 817.12TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 101 of 117 Florida Department of Environmental Protection 9/24/2008 

# 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 Su wannee-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/tm dls/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-driv en or stormwater sources. Consistent with this it only mentions failing septic systems as a po tential 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 su rface water discharges into the Suwannee River Basin. These point sources do not discharge into impa ired 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 di scharge 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 non point 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? Ho w 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 32399-1713TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 102 of 117 Florida Department of Environmental Protection 9/24/2008 In Response to Comments
Thank you for your comments they have been considered an d the document has been edit ed 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 c onsidered as possible sources. The document has been updated to reflect the source of the data (DOH 2007) an d system estimates were included. Thank you for your comments and additional information.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

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Page 104 of 117 Florida Department of Environmental Protection 9/24/2008 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 reduc tion required by EPA you are refe rring 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 Ac t, 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 re duction 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 cont ribute a significant fraction of a pollutant to receiving water
Response to comment 3. The data were used to designate the Suwanne e 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 la nd uses, including roads, contains nutrientts. Additionally, please remember that the st ormwater 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 pr ocess 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 repr esented 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.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

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Page 107 of 117 Florida Department of Environmental Protection 9/24/2008 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 (NO 3 -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 an d 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.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 108 of 117 Florida Department of Environmental Protection 9/24/2008 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 so urces 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..TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 109 of 117 Florida Department of Environmental Protection 9/24/2008 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 fromTMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 110 of 117 Florida Department of Environmental Protection 9/24/2008 the SRP to refine the analysis. As part of that process th e 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 form ed 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.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

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Page 112 of 117 Florida Department of Environmental Protection 9/24/2008 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/L ower 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 FD EP 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 th at 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 in to 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.TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

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Page 115 of 117 Florida Department of Environmental Protection 9/24/2008TMDL Report: Nutrient and Dissolved Oxygen Suwannee River and Santa Fe River

Page 116 of 117 Florida Department of Environmental Protection 9/24/2008 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 ar e 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 me eting 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 li st 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 ar e 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 Suwanne e 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/