Freshwater Flow and Ecological Relationships in Biscayne Bay Contract No. C-15967-WO04-06 Prepared For: Prepared By: In Association With: January 2004 FRESHWATER FLOW AND ECOLOGICAL RELATIONSHIPS IN BISCAYNE BAY Prepared for: SOUTH FLORIDA WATER MANAGEMENT DISTRICT WEST PALM BEACH, FLORIDA Prepared by: BARNES, FERLAND AND ASSOCIATES, INC. 3655 Maguire Boulevard, Suite 150 Orlando, Florida 32803 407-896-8608 In Association with: APPLIED TECHNOLOGY & MANAGEMENT, INC. LEWIS ENVIRONMENTAL SERVICES, INC. Principal Authors: Greg Braun – ATM Roy “Robin” Lewis – LES John Watson – BFA JANUARY 2004 Table of Contents SFWMD Contract No. C-15967-WO04-06 Freshwater Flow and Ecological Relationships in Biscayne Bay Page No. EXECUTIVE SUMMARY ES-1 SECTION 1 – INTRODUCTION 1-1 PROJECT BACKGROUND 1-1 PURPOSE AND SCOPE 1-2 RELATIONSHIPS OF SALINITY, ECOSYSTEMS AND POTENTIAL 1-3 HARM MFL WORK IN OTHER FLORIDA ESTUARINE SYSTEMS 1-4 SECTION 2 – BISCAYNE BAY CHARACTERISTICS 2-1 PROJECT BOUNDARIES AND SUB-REGIONS 2-1 FRESHWATER FLOWS AND SALINITY CONDITIONS 2-11 EXISTING SPECIES/ECOLOGICAL CONDITIONS 2-13 Snake Creek/Oleta River 2-14 Northern Biscayne Bay 2-15 Miami River/Government Cut 2-17 Central Biscayne Bay 2-19 South-Central Biscayne Bay 2-20 Southern Biscayne Bay 2-23 SECTION 3 – SUMMARY OF PROJECT TASKS 3-1 TASK 2 - LITERATURE AND DATA REVIEW 3-1 TASK 3 – INTERVIEWS WITH EXPERTS 3-2 TASK 4 - ALTERNATIVE MFL APPROACHES 3-3 SECTION 4 – VALUED ECOSYSTEM COMPONENTS AND 4-1 CURRENT IMPACTS HABITATS 4-1 Mangrove forests 4-1 Tidal marshes 4-1 Seagrass meadow and macroalgae 4-2 Oyster bars 4-3 Hardbottom 4-4 Freshwater Flow and Ecological Relationships in Biscayne Bay i Table of Contents Softbottom 4-5 POTENTIAL INDICATOR SPECIES 4-5 Micro-organisms 4-5 Foraminifera 4-5 Phytoplankton 4-7 Diatoms 4-7 Listed Species 4-8 American Crocodile 4-12 Roseate Spoonbill 4-14 West Indian Manatee 4-18 Johnson’s Seagrass 4-30 Oysters 4-32 Crustaceans 4-33 Fish 4-39 Seagrass 4-41 SALINITY TOLERANCES, PREFERRED HABITATS AND LIFE 4-42 CYCLES OF POTENTIAL INDICATOR SPECIES OR SUITES OF SPECIES SECTION 5 – POTENTIAL ALTERNATIVE APPROACHES FOR 5-1 MFL DEVELOPMENT FOR BISCAYNE BAY STATIC AND DYNAMIC HABITATS 5-1 VALUED ECOSYSTEM COMPONENTS 5-8 INDICATOR SPECIES 5-9 PRE-DEVELOPMENT SCENARIOS 5-12 ECOLOGICAL PRESERVATION OR STATUS QUO 5-13 REQUIREMENTS FOR PREFERRED FISH COMMUNITIES 5-13 COMMUNITY INDICES 5-14 FOOD WEB SUPPORT 5-14 SOILS 5-14 EVALUATION OF ALTERNATIVE APPROACHES 5-15 SECTION 6 – RECOMMENDED APPROACHES 6-1 SNAKE CREEK/OLETA RIVER 6-3 NORTHERN BISCAYNE BAY 6-3 MIAMI RIVER/GOVERNMENT CUT 6-4 CENTRAL BISCAYNE BAY 6-5 SOUTH-CENTRAL BISCAYNE BAY 6-6 SOUTHERN BISCAYNE BAY 6-7 Freshwater Flow and Ecological Relationships in Biscayne Bay ii Table of Contents SECTION 7 – INFORMATION DEFICIENCIES AND NEEDS 7-1 REFERENCES REF-1 FIGURES DESCRIPTION 1 General Location Map showing Sub-regions 2-2 2 Snake Creek/Oleta River Sub-region 2-4 3 Northern Biscayne Bay Sub-region 2-5 4 Miami River/Government Cut Sub-region 2-6 5 Central Biscayne Bay Sub-region 2-7 6 South-Central Biscayne Bay Sub-region 2-8 7 Southern Biscayne Bay Sub-region 2-9 8 Halophila johnsonii Critical Habitat 2-16 9 Boundaries of Biscayne National Park and Biscayne 2-21 Bay Aquatic Preserve 10 Crocodylus acutus Critical Habitat 2-24 11 Crocodile Sightings and Captures in Biscayne Bay 4-15 12 Crocodile Sightings in Relation to Salinity 4-16 13 a-c Manatee Sightings in Biscayne Bay 4-21 thru 4-23 14 a-b-c-d Essential Manatee Habitat Areas 4-24 thru 4-27 15 Stationary and dynamic habitat components from 5-2 Browder and Moore (1981) 16 Graphic representation of the range of salinity zones 5-3 overlaid on a typical tidal creek system entering a higher salinity habitat. 17 Graphic representation of salinity zones around a 5-4 submerged artesian well in a marine environment. 18 Graphic showing location of seagrass bed in estuary 5-5 19 Graphic showing stationary habitat (seagrass 5-6 meadow) with dynamic habitat (freshwater inflow) overlay and resulting seagrass/ salinity zones under normal flow conditions. Freshwater Flow and Ecological Relationships in Biscayne Bay iii Table of Contents TABLES DESCRIPTION ES-1 Comparison of Relative Strength of Scientific Support for ES-3 the Different MFL Approaches for each Sub-region 1 Other MFL Projects in Estuarine Waters in Florida 1-5 2 Marine and Estuarine Species that are State-listed and/or 4-9 thru Federally-listed Species and which are known to occur in 4-11 Biscayne Bay and/or Adjacent Areas 3a Salinity and Habitat Requirements for Potential Vegetative 4-43 Indicator Species 3b Salinity and Habitat Requirements of Potential Faunal 4-44 thru Indicator Species 4-46 4 Potential Indicator Species for Freshwater MFLs 5-10 thru Establishment in Biscayne Bay 5-11 5 Comparison of Different MFL Approaches for each Sub- 5-16 region 6 Comparison of Relative Strength of Scientific Support for 6-2 the Different MFL Approaches for each Sub-region APPENDICES DESCRIPTION A Task 2 Report – Literature and Data Review B Task 3 Report – Interviews with Experts C Life History Figures of Selected Species D Tables of Bio-indicator Ranking Matrix by Sub- regions E Tables of Advantages & Disadvantages of Different MFL Approaches by Sub-regions Freshwater Flow and Ecological Relationships in Biscayne Bay iv Executive Summary EXECUTIVE SUMMARY The State of Florida has adopted regulations, which require that Water Management Districts identify priority water bodies, establish Minimum Flows and Levels (MFLs) rules for these water bodies and implement these MFLs through water shortage plans and/or the water use permitting process. Specifically, Biscayne Bay has been identified as a priority water body in which an MFL rule is to be developed by the South Florida Water Management District (SFWMD or the District) by December 2004. As one component of the effort to develop an MFL rule for Biscayne Bay, the SFWMD issued a work order to undertake a study entitled, Freshwater Flow and Ecological Relationships in Biscayne Bay. SFWMD entered into an agreement (Contract No. C-15967-WO04-06) with the consultant team of Barnes, Ferland and Associates, Applied Technology Management, Inc. and Lewis Environmental Services, Inc. to conduct a variety of activities which will assist the District in developing the MFL rule for Biscayne Bay. The work conducted by the project team involves the following five tasks: 1) Developing a Project Work Plan 2) Conducting a Literature Search and Data Review 3) Contacting and Interviewing Experts 4) Evaluating Alternative Approaches for District MFL Development 5) Addressing/summarizing Information and Information Needs Tasks 1-4 have been completed and the resulting deliverables for each task were transmitted to the District for review and comment. Questions raised by the District have been addressed, and the Appendices to this report contain the final deliverables for each Task. This document, the Task 5 report, builds on the results of the previous tasks and also includes summaries of pertinent portions of the previously completed tasks. This project has sought to establish a scientific connection between various methods to establish MFLs for Biscayne Bay, and indicators of conditions in the Bay. The recommended over-all process has been to apply numerical rankings to potential indicator species and potential MFL approaches in order to determine the most appropriate approach for each of six sub-regions of the Bay. This is necessary due to the Bay being a large heterogeneous ecosystem that has undergone major anthropogenic changes in the last 100 years. Each of the six identified sub-regions has unique characteristics that demand unique treatment regarding necessary freshwater flows to either maintain existing conditions, or Freshwater Flow and Ecological Relationships in Biscayne Bay ES-1 Executive Summary restore some semblance of historical conditions to allow for a particular ecological function to exist at some level that is acceptable to water managers, citizens and scientists. Table ES-1 shows the highest rated (and therefore recommended) approach(es) for each sub-region, as summarized below: Oleta River/Snake Creek: The recommended approach (Indicator Species) rated highest at 22 with a range of values from 6-22; the indicator species being the American oyster, West Indian Manatee and Johnson's seagrass. Northern Biscayne Bay: The recommended approach (Indicator Species) rated highest at 22 with a range of values from 6-22; the indicator species being the spotted seatrout and manatee grass. Miami River/Government Cut: The recommended approach (Community Index) rated highest at 20 with a range of values from 5-20. This approach utilizes a biodiversity index similar to that developed by Berkely and Campos (1984) for the Bay. Central Biscayne Bay: The recommended approaches (Indicator Species and Valued Ecosystem Component) both rated highest at 22 with a range of values from 5-22. The Indicator Species approach was judged the better of the two by the principal scientists, and the species chosen were pink shrimp and shoal grass. South-Central Biscayne Bay: The recommended approach (Valued Ecosystem Component) rated highest at 22 with a range of values from 5-22; the VEC being a sustainable pink shrimp harvest. Southern Biscayne Bay: The recommended approach (Food Web Support) rated highest at 26 with a range of values from 5-26. The intent is that the forage fish food base be sustained to support: (1) nesting productivity for the Roseate Spoonbill (and several