| Table of Contents Suwannee River Basin SWIM Plan Update Page Executive Summary ................................................................................................... vii 1.0 Introduction .......................................................................................................... 1 1.1 The SWIM Act - Purpose and Intent ........................................................................ 1 1.2 SWIM in the Suwannee River Water Management District ...................................... 3 1.2.1 Previous SWIM Plans .................................................................................... 4 1.2.2 SWIM Plan Update and Consolidation ........................................................... 6 1.2.3 Integrating Water Management and the Economy ......................................... 7 1.2.3.1 Preserving Working Forests to Protect Water Quantity and Quality .. 8 1.2.3.2 Improving Water Quality to Promote Aquaculture in Coastal Communities .................................................................................... 9 1.2.3.3 Innovative Agricultural Practices to Promote a Sustainable Regional Economy ......................................................................... 10 1.2.3.4 Springs-Based Recreation and Tourism ......................................... 11 1.2.3.5 Hydrologic Restoration and Aquifer Recharge ................................ 12 1.2.3.6 Summary ........................................................................................ 13 1.3 Suwannee River Basin Planning Area Description ................................................. 13 1.3.1 Physiography and Topography .................................................................... 15 1.3.2 Hydrogeology .............................................................................................. 16 1.3.3 Hydrology and Water Chemistry .................................................................. 17 1.3.4 Natural Systems .......................................................................................... 18 1.3.4.1 Upland Habitats .............................................................................. 18 1.3.4.2 Freshwater Habitats........................................................................ 19 1.3.4.3 Marine/Estuarine Habitats .............................................................. 21 1.3.5 Land Use ..................................................................................................... 21 2.0 Issues and Drivers ............................................................................................. 27 2.1 Water Quantity ....................................................................................................... 27 2.1.1 Regulatory Framework ................................................................................ 28 2.1.1.1 Minimum Flows and Minimum Water Levels (MFLs) ....................... 28 2.1.1.2 Consumptive Use ........................................................................... 29 2.1.2 Status and Trends ....................................................................................... 29 2.1.2.1 Upper Suwannee River ................................................................... 30 2.1.2.2 Alapaha River ................................................................................. 31 2.1.2.3 Withlacoochee River and Madison Blue Spring .............................. 32 2.1.2.4 Middle Suwannee River .................................................................. 33 2.1.2.5 Santa Fe River System ................................................................... 35 2.1.2.6 Lower Suwannee River, Fanning/Little Fanning Spring, and Manatee Spring .............................................................................. 36 2.1.3 Regulatory Issues ........................................................................................ 38 2.1.4 Threats to Water Quantity ............................................................................ 40 2.2 Water Quality ......................................................................................................... 41 2.2.1 Regulatory Framework ................................................................................ 41 2.2.2 Status and Trends ....................................................................................... 41 2.2.2.1 Nitrate in Rivers and Streams ......................................................... 42 Suwannee River Basin SWIM Plan Update i ESA / D150586.00 Final November 2017 Table of Contents 2.2.2.2 Phosphorus in Rivers and Streams ................................................. 48 2.2.2.3 Nitrate in Springs ............................................................................ 48 2.2.3 Regulatory Issues ........................................................................................ 54 2.2.3.1 Impairments .................................................................................... 54 2.2.3.2 Potential Effects of Revisions to Water Quality Standards .............. 54 2.2.3.3 Total Maximum Daily Loads (TMDLs) and Basin Management Action Plans (BMAPs) .................................................................... 57 2.2.4 Threats to Water Quality ............................................................................... 60 2.3 Natural Systems .................................................................................................... 63 2.3.1 Upland Habitats ........................................................................................... 64 2.3.2 Freshwater Habitats .................................................................................... 68 2.3.3 Marine/ Estuarine Habitats .......................................................................... 76 2.3.3.1 Tidal Wetlands ................................................................................ 77 2.3.3.2 Hard and Soft Bottom Habitats ....................................................... 79 2.3.3.3 Seagrass Beds ............................................................................... 83 2.3.4 Listed Species ............................................................................................. 84 2.3.5 Threats to Natural Systems ......................................................................... 86 2.3.5.1 Land Use Changes ......................................................................... 87 2.3.5.2 Declines in Water Quantity and Quality .......................................... 88 2.3.5.3 Introduction of Non-Native and Invasive Species ............................ 89 2.3.5.4 Climate Change .............................................................................. 90 3.0 Management Actions ......................................................................................... 93 3.1 Water Quantity ....................................................................................................... 93 3.2 Water Quality ......................................................................................................... 95 3.3 Natural Systems .................................................................................................... 96 4.0 Projects and Initiatives .................................................................................... 100 4.1 Ongoing Projects and Initiatives ........................................................................... 100 4.1.1 Water Quantity........................................................................................... 100 4.1.2 Water Quality ............................................................................................. 107 4.1.3 Natural Systems ......................................................................................... 113 4.2 Proposed Projects ............................................................................................... 116 4.2.1 Water Quantity........................................................................................... 116 4.2.2 Water Quality ............................................................................................. 125 4.2.3 Natural systems ......................................................................................... 131 List of Figures 1. District boundary. ........................................................................................................................ 4 2. Consolidated Suwannee River Basin Watersheds .................................................................. 14 3. Physiographic Regions of the District (District 2010). .............................................................. 16 4. Confinement Conditions of the UFA within the District (confinement conditions from Miller, 1986) ..................................................................................................................... 17 5. Land use/ Land cover in the Suwannee River Basin in 1995. ................................................. 22 6. Land use/ Land cover in the Suwannee River Basin in 2011 (note: the watershed boundary extends beyond the District land use coverage available). ............................ 23 7. Extent of publicly owned conservation lands in the Suwannee River Basin (FDEP and DMS 2016 ........................................................................................................................ 25 8. Suwannee River Basin in Florida and Georgia (HSW Draft MFL Report 2016). ..................... 31 9. Total extent of the Alapaha River drainage watershed.