MINIMUM FLOWS AND MINIMUM WATER LEVELS RE-EVALUATION FOR THE LOWER SANTA FE AND ICHETUCKNEE RIVERS AND PRIORITY SPRINGS DRAFT DECEMBER 2019 Prepared for: Suwannee River Water Management District 9225 County Road 49 Live Oak, Florida 32060 Prepared by: 15711 Mapledale Blvd, Suite B Tampa, Florida 33624 Minimum Flows and Minimum Water Levels Re-evaluation for the Lower Santa Fe and Ichetucknee Rivers and Priority Springs – Draft – December 2019 CONTENTS 1. INTRODUCTION .............................................................................................. 1 1.1 Watershed and River Descriptions .................................................................................. 2 1.2 Study Area ....................................................................................................................... 2 2. HYDROLOGY .................................................................................................. 4 2.1 Physiography ................................................................................................................... 4 2.2 Hydrogeology .................................................................................................................. 4 2.3 Hydrologic Characteristics ............................................................................................... 8 2.3.1 Stream Discharge and Stage .......................................................................................... 8 2.3.2 Infilling of Ichetucknee River Data at HWY 27 Near Hildreth Gage ............................. 12 2.3.3 Watershed Yield .......................................................................................................... 12 2.3.4 Atlantic Multidecadal Oscillation ................................................................................. 14 2.3.5 Rainfall and Air Temperature ...................................................................................... 14 2.3.6 Groundwater level ....................................................................................................... 18 2.4 Priority Springs .............................................................................................................. 18 2.5 Surface Water Quality ................................................................................................... 22 2.6 Groundwater Use .......................................................................................................... 23 2.7 Reference Timeframe Flow ........................................................................................... 24 2.7.1 Flow Characteristics ..................................................................................................... 26 3. BIOLOGY ...................................................................................................... 29 3.1 Conceptual Ecological System Model ........................................................................... 29 3.2 Riverine and Riparian Habitats ...................................................................................... 31 3.2.1 Lower Santa Fe River ................................................................................................... 32 3.2.2 Ichetucknee River ........................................................................................................ 36 3.3 Floodplain habitat ......................................................................................................... 36 3.4 Aquatic Biota ................................................................................................................. 38 3.4.1 Submerged Aquatic Vegetation ................................................................................... 38 3.4.2 Aquatic Macroinvertebrates ........................................................................................ 44 3.4.3 Fish ............................................................................................................................... 44 3.4.4 Threatened and Endangered Species .......................................................................... 46 3.4.5 Manatee....................................................................................................................... 48 HSW Engineering, Inc. ■ www.hsweng.com 2 Engineering and scientific solutions within your reach… Minimum Flows and Minimum Water Levels Re-evaluation for the Lower Santa Fe and Ichetucknee Rivers and Priority Springs – Draft – December 2019 3.4.6 Ichetucknee Siltsnail .................................................................................................... 51 3.4.7 Oval Pigtoe ................................................................................................................... 52 3.4.8 Gulf Sturgeon ............................................................................................................... 53 3.4.9 Suwannee Bass ............................................................................................................ 53 3.4.10 Seasonality ................................................................................................................... 55 4. APPROACH TO SETTING MFLS ...................................................................... 56 4.1 Identification of Relevant WRVs ................................................................................... 56 4.1.1 Recreation in and On the Water (WRV 1) ................................................................... 56 4.1.2 Fish and Wildlife Habitats and the Passage of Fish (WRV 2) ....................................... 56 4.1.3 Estuarine Resources (WRV 3) ...................................................................................... 57 4.1.4 Transfer of Detrital Material (WRV 4) ......................................................................... 57 4.1.5 Maintenance of Freshwater Storage (WRV 5) ............................................................. 57 4.1.6 Aesthetic and Scenic Attributes (WRV 6) .................................................................... 57 4.1.7 Filtration and Absorption of Nutrients and Other Pollutants (WRV 7) ....................... 57 4.1.8 Sediment Loads (WRV 8) ............................................................................................. 57 4.1.9 Water Quality (WRV 9) ................................................................................................ 58 4.1.10 Navigation (WRV 10) ................................................................................................... 58 4.1.11 WRV Summary ............................................................................................................. 58 4.2 Indicators and Response Functions ............................................................................... 58 4.3 Modeling ....................................................................................................................... 62 4.3.1 HEC-RAS Modeling ....................................................................................................... 62 4.3.2 SEFA Modeling ............................................................................................................. 71 4.4 MFLs Assessment Methods ........................................................................................... 73 5. EVALUATION OF WRVS ................................................................................ 75 5.1 Recreation In and On the Water ................................................................................... 76 5.2 Fish Passage and Fish and Wildlife Habitat ................................................................... 79 5.2.1 Fish Passage ................................................................................................................. 79 5.2.2 Gulf Sturgeon Passage ................................................................................................. 80 5.2.3 Instream Habitat .......................................................................................................... 81 5.2.4 Woody habitat ............................................................................................................. 84 5.2.5 Manatee Thermal Refuge ............................................................................................ 86 5.2.6 Floodplain Habitat ....................................................................................................... 87 HSW Engineering, Inc. ■ www.hsweng.com 3 Engineering and scientific solutions within your reach… Minimum Flows and Minimum Water Levels Re-evaluation for the Lower Santa Fe and Ichetucknee Rivers and Priority Springs – Draft – December 2019 5.2.7 Hydric Soils................................................................................................................... 88 5.2.8 Submerged Aquatic Vegetation ................................................................................... 91 5.3 Sediment Loads ............................................................................................................. 92 5.4 Water Quality ................................................................................................................ 93 5.5 Resources Upstream from US441 ................................................................................. 95 6. RIVER MFLS DEVELOPMENT ......................................................................... 99 6.1 Introduction ..................................................................................................................