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Recommended Minimum Flows for the Homosassa River System

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Recommended Minimum Flows for the Homosassa River System Recommended Minimum Flows for the Homosassa River System October 30, 2012 Douglas A. Leeper, Michael S. Flannery, Michael G. Heyl, Ron Basso Southwest Florida Water Management District Brooksville, Florida and Marty Kelly Formerly with the Southwest Florida Water Management District with contributions by HSW Engineering, Inc. Tampa, Florida Recommended Minimum Flows for the Homosassa River System October 30, 2012 Douglas A. Leeper, Michael S. Flannery, Michael G.Heyl, Ron Basso Southwest Florida Water Management District Brooksville, Florida and Marty Kelly Formerly with the Southwest Florida Water Management District with contributions by HSW Engineering, Inc. Tampa, Florida The Southwest Florida Water Management District (District) does not discriminate upon the basis of any individual‟s disability status. This non-discriminatory 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 accommodation as provided for in the American with Disabilities Act should contact (352) 796-7211 or 1-800-423-1476, extension 4215; TDD ONLY 1-800-231-6103; FAX (352) 754-6749. On the Cover: Aerial photograph of the Homosassa Main Springs pool and upper portion of the Homosassa River in 2001 (Southwest Florida Water Management District files). Page 1 Table of Contents Page Title Page .................................................................................................................................... 1 Table of Contents ........................................................................................................................ 2 List of Tables .............................................................................................................................. 7 List of Figures ........................................................................................................................... 13 Acknowledgements ................................................................................................................... 19 Executive Summary ................................................................................................................ 20 CHAPTER 1. Minimum Flows and Levels and Purpose of this Report ...................................23 1.1 Legal Directives and Use of Minimum Flows and Levels .............................................23 1.2 Development of Minimum Flows and Levels in the Southwest Florida Water Management District ...................................................................................................23 1.2.1 District Minimum Flows and Levels Rules and Documents ..................................23 1.2.2 Conceptual Overview of Minimum Flows .............................................................24 1.2.3 Significant Harm ..................................................................................................25 1.3 Purpose of this Report ................................................................................................26 CHAPTER 2. Physical Setting and Description of the Homosassa River System ...................28 2.1 Location and General Description ...............................................................................28 2.2 Physiography, Watershed and Springshed .................................................................35 2.3 Watershed Land Use and Cover .................................................................................37 2.4 Hydrology ...................................................................................................................39 2.4.1 Data Sources for Hydrologic Information ..............................................................39 2.4.2 Climate and Rainfall .............................................................................................43 2.4.3 Stage and Tides ...................................................................................................46 2.4.4 Discharge – Mean Daily Records .........................................................................49 2.4.5 Discharge – Historical Instantaneous Records .....................................................55 2.4.6 Discharge – Consideration of Mean Daily Records and Historical Instantaneous Records ........................................................................................61 2.4.7 Discharge – Relationships with Rainfall and Groundwater Levels ........................62 2.4.8 Discharge – Water Use Impacts on Spring Discharge ..........................................64 2.5 Bathymetry and River-Kilometer System .....................................................................68 2.6 Bottom Substrates ......................................................................................................72 2.7 Shoreline ....................................................................................................................73 2.8 Water Quality ..............................................................................................................76 2.8.1 Water Classification and Quality ..........................................................................76 2.8.2 Data Sources for Water Quality Summaries .........................................................77 2.8.3 Spring Water Quality ............................................................................................80 2.8.4 River Temperature ...............................................................................................85 2.8.5 Modeling River Temperature ................................................................................86 2.8.6 River Salinity ........................................................................................................89 2.8.7 Modeling River Salinity – Empirical Regression Models .......................................95 2.8.8 Modeling River Salinity – Hydrodynamic Model ...................................................96 2.8.9 Modeling River Salinity – Comparison of Hydrodynamic and Empirical Regression Models ............................................................................................ 101 2.8.10 Other River Water Quality Characteristics .......................................................... 103 Page 2 CHAPTER 3. Biological Characteristics of the Homosassa River System ............................ 107 3.1 Vegetation ................................................................................................................ 107 3.1.1 Description ......................................................................................................... 107 3.1.2 Relationships Between Vegetation, Salinity and Other Physiochemical Variables ............................................................................................................ 108 3.2 Benthic Macroinvertebrates ...................................................................................... 115 3.2.1 Description ......................................................................................................... 115 3.2.2 Relationships Between Benthic Invertebrates, Salinity and Other Physiochemical Variables .................................................................................. 126 3.3 Fish and Invertebrate Plankton and Nekton .............................................................. 127 3.3.1 Description ......................................................................................................... 127 3.3.2 Relationships Between Fish and Invertebrate Nekton and Plankton and Inflow . 131 3.4 Manatees .................................................................................................................. 138 3.4.1 Description ......................................................................................................... 138 3.4.2 Relationships Between Manatees and Inflow ..................................................... 140 CHAPTER 4. Resources of Concern and Technical Approach for Developing recommended minimum flows ............................................................................................... 141 4.1 Resources of Concern .............................................................................................. 141 4.2 Fish and Invertebrate Plankton and Nekton Criteria and Technical Approach ........... 141 4.3 Salinity-Based Habitat Criteria and Technical Approach ........................................... 142 4.4 Manatee Thermal Refuge Criteria and Technical Approach ...................................... 145 CHAPTER 5. Results and Initial Recommended Minimum Flows ......................................... 148 5.1 Introduction ............................................................................................................... 148 5.2 Results for Fish and Invertebrate Plankton and Nekton Analyses ............................. 148 5.3 Results for Salinity-Based Habitat Analyses.............................................................. 151 5.3.1 Overview ............................................................................................................ 151 5.3.2 Isohaline Locations – 5 to 30 Percent Flow Reduction Results .......................... 152 5.3.3 Note Concerning Use of Hydrodynamic Modeling Results for Habitats Associated with Salinities of 2 or Less ............................................................... 152 5.3.4 Salinity-Based Bottom Habitats – 5 to 30 Percent Flow Reduction Results .......
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