MINIMUM FLOWS AND MINIMUM WATER LEVELS RE-EVALUATION FOR THE LOWER SANTA FE AND ICHETUCKNEE RIVERS AND PRIORITY SPRINGS FINAL (with minor revisions) JANUARY 2021 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 ADA Statement Americans with Disabilities Act: The District does not discriminate upon the basis of any individual’s disability status. This nondiscrimination policy involves every aspect of the District’s functions including one’s access to, participation, employment, or treatment in its programs or activities. Anyone requiring reasonable accommodation as provided for in the Americans with Disabilities Act should contact the District at 386.362.1001 or 800.226.1066 (Florida only). The District’s fax number is 386.362.1056. ERRATA (revisions from original version) Document Location Revision Reason for Revision Page 10, Bullet 2, Line 3 9.0% changed to 9.1% to correct a rounding error Page 11, Table, Row 5 9.0% changed to 9.1% to correct a rounding error Page 11, Paragraph 1, Line 7 9.0% changed to 9.1% to correct a rounding error Page 24, Paragraph 2, Line 3 (SRWMD 2013) removed to correct a reference Page 113, Bullet 2, Line 1 9.0% changed to 9.1% to correct a rounding error Page 113, Table 33, Row 5 9.0% changed to 9.1% to correct a rounding error Page 114, Paragraph 6, Line 2 9.0% changed to 9.1% to correct a rounding error Page 114, Paragraph 7, Line 1 347 changed to 346 to correct a rounding error Page 122, Bullet 2, Line 4 9.0% changed to 9.1% to correct a rounding error Page 122, Bullet 3, Line 2 Mission added Mission Spring inadvertently omitted Page 122, Bullet 3, Line 3 347 changed to 346 to correct a rounding error Minimum Flows and Minimum Water Levels Re-evaluation for the Lower Santa Fe and Ichetucknee Rivers and Priority Springs – January 2021 CONTENTS 1. INTRODUCTION .............................................................................................. 1 1.1 Watershed and River Descriptions .................................................................................. 2 1.2 Study Area ....................................................................................................................... 3 2. HYDROLOGY .................................................................................................. 5 2.1 Physiography ................................................................................................................... 5 2.2 Hydrogeology .................................................................................................................. 6 2.3 Hydrologic Characteristics ............................................................................................... 7 2.3.1 Stream Discharge and Stage .......................................................................................... 7 2.3.2 Infilling of Ichetucknee River Data at HWY 27 Near Hildreth Gage ............................. 13 2.3.3 Watershed Yield .......................................................................................................... 15 2.3.4 Atlantic Multidecadal Oscillation ................................................................................. 16 2.3.5 Rainfall and Air Temperature ...................................................................................... 20 2.3.6 Groundwater level ....................................................................................................... 23 2.4 Priority Springs .............................................................................................................. 23 2.5 Surface Water Quality ................................................................................................... 27 2.6 Groundwater Use .......................................................................................................... 28 2.7 Reference Timeframe Flow ........................................................................................... 29 2.7.1 Flow Characteristics ..................................................................................................... 31 3. BIOLOGY ...................................................................................................... 36 3.1 Conceptual Ecological System Model ........................................................................... 36 3.2 Riverine and Riparian Habitats ...................................................................................... 38 3.2.1 Lower Santa Fe River ................................................................................................... 39 3.2.2 Ichetucknee River ........................................................................................................ 43 3.3 Floodplain habitat ......................................................................................................... 43 3.4 Aquatic Biota ................................................................................................................. 44 3.4.1 Submerged Aquatic Vegetation ................................................................................... 44 3.4.2 Aquatic Macroinvertebrates ........................................................................................ 51 3.4.3 Fish ............................................................................................................................... 51 3.4.4 Threatened and Endangered Species .......................................................................... 54 3.4.5 Manatee....................................................................................................................... 55 3.4.6 Ichetucknee Siltsnail .................................................................................................... 58 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 – January 2021 3.4.7 Oval Pigtoe ................................................................................................................... 59 3.4.8 Gulf Sturgeon ............................................................................................................... 60 3.4.9 Suwannee Bass ............................................................................................................ 60 3.4.10 Seasonality ................................................................................................................... 62 4. APPROACH TO SETTING MFLS ...................................................................... 63 4.1 Identification of Relevant WRVs ................................................................................... 63 4.1.1 Recreation in and On the Water (WRV 1) ................................................................... 63 4.1.2 Fish and Wildlife Habitats and the Passage of Fish (WRV 2) ....................................... 63 4.1.3 Estuarine Resources (WRV 3) ...................................................................................... 64 4.1.4 Transfer of Detrital Material (WRV 4) ......................................................................... 64 4.1.5 Maintenance of Freshwater Storage (WRV 5) ............................................................. 64 4.1.6 Aesthetic and Scenic Attributes (WRV 6) .................................................................... 64 4.1.7 Filtration and Absorption of Nutrients and Other Pollutants (WRV 7) ....................... 64 4.1.8 Sediment Loads (WRV 8) ............................................................................................. 65 4.1.9 Water Quality (WRV 9) ................................................................................................ 65 4.1.10 Navigation (WRV 10) ................................................................................................... 65 4.1.11 WRV Summary ............................................................................................................. 65 4.2 Indicators and Response Functions ............................................................................... 65 4.3 Modeling ....................................................................................................................... 69 4.3.1 HEC-RAS Modeling ....................................................................................................... 69 4.3.2 SEFA Modeling ............................................................................................................. 78 4.4 MFLs Assessment Methods ........................................................................................... 80 4.5 Uncertainty and Adaptive Management ....................................................................... 81 5. EVALUATION OF WRVS ................................................................................ 84 5.1 Recreation In and On the Water ................................................................................... 84 5.2 Fish Passage and Fish and Wildlife Habitat ................................................................... 88 5.2.1 Fish Passage ................................................................................................................. 88 5.2.2 Gulf Sturgeon Passage ................................................................................................. 89 5.2.3 Instream Habitat .........................................................................................................