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Freshwater Inflow Effects on Fishes and Invertebrates in the Chassahowitzka River and Estuary

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FRESHWATER INFLOW EFFECTS ON FISHES AND INVERTEBRATES IN THE CHASSAHOWITZKA RIVER AND ESTUARY M.F.D. Greenwood1; E.B. Peebles2; S.E. Burghart2; T.C. MacDonald1; R.E. Matheson, Jr.1; R.H. McMichael, Jr.1 1Florida Fish and Wildlife Conservation Commission Fish and Wildlife Research Institute 100 Eighth Avenue Southeast St. Petersburg, Florida 33701-5095 2University of South Florida College of Marine Science 140 Seventh Avenue South St. Petersburg, Florida 33701-5016 Prepared for The Southwest Florida Water Management District 2379 Broad Street Brooksville, Florida 34609-6899 SWFWMD Agreement No. 05CON000117 September 2008 TABLE OF CONTENTS SUMMARY...................................................................................................................... v LIST OF FIGURES..........................................................................................................xi LIST OF TABLES..........................................................................................................xiii 1.0 INTRODUCTION .................................................................................................. 1 1.1 Objectives.................................................................................................. 2 2.0 METHODS............................................................................................................ 5 2.1 Study Area ................................................................................................. 5 2.2 Survey Design ........................................................................................... 7 2.3 Plankton Net Specifications and Deployment ............................................ 9 2.4 Seine and Trawl Specifications and Deployment..................................... 10 2.5 Plankton Sample Processing ................................................................... 11 2.5.1 Staging Conventions .................................................................. 12 2.6 Seine and Trawl Sample Processing. ...................................................... 16 2.7 Data Analysis........................................................................................... 17 2.7.1 Freshwater Inflow (F).................................................................. 17 2.7.2 Organism-Weighted Salinity (SU)............................................... 17 2.7.3 Center of CPUE (kmU)............................................................... 18 2.7.4 Organism Number (N) and Relative Abundance (N¯ ) ................. 18 2.7.5 Inflow Response Regressions .................................................... 19 2.7.6 Community-level Analyses ......................................................... 20 2.7.6.1. Plankton................................................................... 20 2.7.6.2 Seines and Trawls ................................................... 21 2.7.7 Data Limitations and Gear Biases .............................................. 22 3.0 RESULTS AND DISCUSSION ........................................................................... 25 3.1 Streamflow Status During Survey Years.................................................. 25 i 3.2 Physico-chemical Conditions ................................................................... 25 3.3 Catch Composition .................................................................................. 30 3.3.1 Fishes......................................................................................... 30 3.3.1.1 Plankton net............................................................. 30 3.3.1.2 Seine ....................................................................... 30 3.3.1.3 Trawl........................................................................ 31 3.3.2. Invertebrates. ............................................................................. 31 3.3.2.1. Plankton net............................................................. 31 3.3.2.2. Seine. ...................................................................... 31 3.3.2.3. Trawl........................................................................ 31 3.4 Use of Area as Spawning Habitat ............................................................ 32 3.5 Use of Area as Nursery Habitat ............................................................... 33 3.6 Seasonality .............................................................................................. 33 3.6.1. Plankton Net............................................................................... 33 3.6.2. Seine and Trawl ......................................................................... 37 3.6.2. Seine and Trawl ......................................................................... 37 3.7 Distribution (kmu) Responses to Freshwater Inflow................................. 41 3.7.1 Plankton Net............................................................................... 41 3.7.2 Seine and Trawl ......................................................................... 41 3.8 Abundance (N, N¯ ) Responses to Freshwater Inflow ............................... 42 3.8.1 Plankton Net............................................................................... 42 3.8.2 Seine and Trawl ......................................................................... 44 3.9 Community Structure ............................................................................... 48 3.9.1 Plankton Net Community Heterogeneity (H) Responses to Freshwater Inflow (F3) ................................................................ 48 3.9.2. Community structure: seine and trawl ........................................ 52 4.0 CONCLUSIONS ................................................................................................. 61 4.1 Descriptive Observations......................................................................... 61 ii 4.2 Responses to Freshwater Inflow.............................................................. 63 4.3 Community Structure ............................................................................... 65 4.4 Synthesis ................................................................................................. 66 5.0 REFERENCES................................................................................................... 69 Appendix A: Plankton data summary tables................................................................A-1 Appendix B: Seine and trawl summary tables .............................................................B-1 Appendix C: Length-frequency plots for selected taxa ............................................... C-1 Appendix D: Seine catch overview plots .................................................................... D-1 Appendix E: Trawl catch overview plots ......................................................................E-1 Appendix F: Plots of plankton-net distribution responses............................................F-1 Appendix G: Plots of the seine and trawl distribution responses................................. G-1 Appendix H: Plots of plankton-net abundance responses.......................................... H-1 Appendix I: Plots of the seine and trawl abundance responses ...................................I-1 iii iv SUMMARY Quantitative ecological criteria are needed to establish minimum flows and levels for rivers and streams within the Southwest Florida Water Management District (SWFWMD), as well as for the more general purpose of improving overall management of aquatic ecosystems. As part of the approach to obtaining these criteria, the impacts of managed freshwater inflows on downstream estuaries are being assessed. A two year study of freshwater inflow effects on habitat use by estuarine organisms in the Chassahowitzka River estuary was undertaken from August 2005 to July 2007. The general objective of the present data analysis was to identify patterns of estuarine habitat use and organism abundance under variable freshwater inflow conditions and to evaluate responses. Systematic monitoring was performed to develop a predictive capability for evaluating potential impacts of proposed freshwater withdrawals and, in the process, to contribute to baseline data. The predictive aspect involves development of regressions that describe variation in organism distribution and abundance as a function of natural variation in inflows. These regressions can be applied to any proposed alterations of freshwater inflows that fall within the range of natural variation documented during the data collection period. For sampling purposes, the Chassahowitzka River estuary was divided into five zones from which plankton net, seine net and trawl samples were taken. Sampling was conducted on a monthly basis for the first year of the study (August 2005 to July 2006) and every six weeks for the remainder of the study (August 2006 to July 2007). Salinity, water temperature, dissolved oxygen and pH measurements were taken in association with each net deployment. Daily freshwater inflow estimates for the Chassahowitzka River estuary were derived from gauged streamflow records (USGS gauge 02310650) with missing data estimated by interpolation or from maximum daily stage in the Chassahowitzka River and water level at the Weeki Wachee well. A large body of descriptive habitat-use information was generated and is presented in accompanying appendices. v Larval gobies and anchovies dominated the plankton net’s larval fish catch. Gobiosoma and Microgobius were the dominant goby taxa, and the anchovies
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