Proposed Minimum Flows for the Pithlachascotee River - Revised Draft Report for Peer Review August 29, 2016 1 Proposed Minimum Flows for the Pithlachascotee River - Revised Draft Report for Peer Review August 29, 2016 Doug Leeper, Gabriel Herrick, Ron Basso, Mike Heyl, Yonas Ghile Southwest Florida Water Management District Brooksville Florida and Michael Flannery, Tammy Hinkle, Jason Hood and Gary Williams, Ph.D. Formerly with the Southwest Florida Water Management District With contributions by HDR Engineering, Inc. Tampa, Florida The Southwest Florida Water Management District (District) does not discriminate on the basis of disability. This nondiscrimination policy involves every aspect of the District’s functions, including access to and participation in the District’s programs and activities. Anyone requiring reasonable accommodation as provided for in the Americans with Disabilities Act should contact the District’s Human Resources Bureau Chief, 2379 Broad St., Brooksville, FL 34604-6899; telephone (352) 796- 7211 or 1-800-423-1476 (FL only), ext. 4703; or email [email protected]. If you are hearing or speech impaired, please contact the agency using the Florida Relay Service, 1-800-955- 8771 (TDD) or 1-800-955-8770 (Voice). 2 TABLE OF CONTENTS List of Appendices ................................................................................................................................ 5 Acknowledgements .............................................................................................................................. 7 List of Abbreviations and Acronyms ..................................................................................................... 8 Executive Summary ............................................................................................................................. 9 Introduction: Context and Purpose .................................................................................. 11 Purpose .................................................................................................................................... 11 Legal Mandates ........................................................................................................................ 11 Flow Definitions and Concepts ................................................................................................. 13 Overview of Methods and Assumptions ................................................................................... 14 Fundamental Assumptions ................................................................................................. 15 Significant Harm ................................................................................................................. 15 Baseline Flows and Conditions .......................................................................................... 16 Building Block Approach .................................................................................................... 16 Minimum Flow Thresholds ................................................................................................. 16 Percent-of-Flow Method and 15 Percent Change Criteria ................................................. 17 Vertical Datums ........................................................................................................................ 18 Background: Pithlachascotee River Watershed Characteristics ..................................... 20 Introduction ............................................................................................................................... 20 Watershed Size and Location ................................................................................................... 20 Climate ...................................................................................................................................... 21 Physiography ............................................................................................................................ 22 Hydrogeology ............................................................................................................................ 23 Land Use/Cover ........................................................................................................................ 23 Regional Water Withdrawals .................................................................................................... 25 Flow Characteristics ................................................................................................................. 28 Mean Flow Rates and Area-Based Runoff ......................................................................... 30 Seasonal Flow Characteristics ........................................................................................... 31 Flows Before and After Relocation of the Long-term Streamflow Gage ............................ 31 Model Simulations of the Effects of Historical Groundwater Pumping on River Flows ............. 33 Numerical Models .............................................................................................................. 33 Numerical Modeling to Estimate Effects of Historic Groundwater Withdrawals ................. 35 Water Quality .......................................................................................................................... 36 Water Body Classification ................................................................................................ 36 Water Quality Trends ....................................................................................................... 37 Dissolved Oxygen ............................................................................................................ 42 Background: Lower Pithlachascotee River Characteristics ............................................. 45 Lower River Physiography ........................................................................................................ 45 Tides ......................................................................................................................................... 46 Bathymetry ................................................................................................................................ 47 Benthic Substrates and Organisms .......................................................................................... 50 Shoreline Characteristics .......................................................................................................... 51 Salinity ...................................................................................................................................... 54 Salinity at USGS Gages ..................................................................................................... 54 Salinity at District Mid-Channel Stations ............................................................................ 56 Methods: Resources of Concern and Technical ApproacH ............................................ 60 Study Area ................................................................................................................................ 60 Baseline Flows for Minimum Flows Analyses ........................................................................... 61 Seasonal Flow Blocks ............................................................................................................... 65 Resources of Concern and Methods for Determining Minimum Flows for the Upper, Freshwater Segment of the Pithlachascotee River ......................................................................... 66 3 Resources of Concern for the Upper River ........................................................................ 66 Methods for the Upper River .............................................................................................. 68 Resources of Concern and Methods for Determining Minimum Flows for the Lower, Estuarine Segment of the Pithlachascotee River ............................................................................................ 79 Resources of Concern for the Lower River ........................................................................ 79 Methods for the Lower River .............................................................................................. 81 Results of the Minimum Flows Analyses and Recommened Minimum Flows................. 88 Introduction ............................................................................................................................... 88 Results of Minimum Flows Analyses for the Upper River ......................................................... 88 Minimum Low Flow Threshold Results .............................................................................. 88 Percent-of-Flow: Instream PHABSIM Results .................................................................... 90 Percent-of-Flow: Additional Instream and Woody Habitat Inundation Results ................... 92 Percent-of-Flow: Floodplain Habitat Inundation and Minimum High Flow Threshold Results .................................................................................................................................................... 96 Summary of Proposed Minimum Flows for the Upper River ................................................... 101 Protection of Environmental Values for the Upper River ........................................................ 103 Results of Minimum Flows Analysis of the Lower River