ISSN 1930-1448 FISH AND WILDLIFE RESEARCH INSTITUTE TECHNICALTECHNICAL REPORTSREPORTS Seagrass Integrated Mapping and Monitoring Program Mapping and Monitoring Report No. 2 Laura A. Yarbro and Paul R. Carlson, Jr. Editors Florida Fish and Wildlife Conservation Commission FWRI Technical Report TR-17 version 2.0 2016 Rick Scott Governor of Florida Florida Fish and Wildlife Conservation Commission Nick Wiley Executive Director Gil McRae Fish and Wildlife Research Institute Director The Fish and Wildlife Research Institute (FWRI) is a division of the Florida Fish and Wildlife Conservation Commission (FWC). The FWC is “managing fish and wildlife resources for their long-term well-being and the benefit of people.” The FWRI conducts applied research pertinent to managing fishery resources and species of special concern in Florida. Programs at FWRI focus on obtaining the data and information that managers of fish, wildlife, and ecosystem resources need to sustain Florida's natural resources. Topics include managing recreationally and commercially important fish and wildlife species; preserving, managing, and restoring terrestrial, freshwater, and marine habitats; collecting information related to popula- tion status, habitat requirements, life history, and recovery needs of upland and aquatic species; synthesizing ecological, habitat, and socioeconomic information; and developing educational and outreach programs for classroom educators, civic organizations, and the public. The FWRI publishes three series: Memoirs of the Hourglass Cruises, Florida Marine Research Publications, and FWRI Technical Reports. FWRI Technical Reports contain information relevant to immediate resource-management needs. Seagrass Integrated Mapping and Monitoring Program Mapping and Monitoring Report No. 2 Laura A. Yarbro Paul R. Carlson, Jr. Editors Florida Fish and Wildlife Conservation Commission Fish and Wildlife Research Institute 100 Eighth Avenue Southeast St. Petersburg, Florida 33701 USA Florida Fish and Wildlife Conservation Commission FWRI Technical Report TR–17.2 2016 Front Cover Photograph Foraminifera (Archaias spp.) on blade of stargrass Halophila engelmannii Back Cover Photograph Starfish (Echinaster sentus) in bed of shoalgrass Halodule wrightii and green macroalgae Caulerpa prolifera Paul Carlson, Jr., FWC Fish and Wildlife Research Institute Copies of this document may be obtained from http://research.myfwc.com Florida Fish and Wildlife Conservation Commission Fish and Wildlife Research Institute 100 Eighth Avenue SE St. Petersburg, FL 33701-5020 USA Attn: Librarian Document Citation Yarbro, L. A., and P. R. Carlson, Jr., eds. 2016. Seagrass Integrated Mapping and Monitoring Program: Mapping and Monitoring Report No. 2. Fish and Wildlife Research Institute Technical Report TR-17 version 2. vi + 281 p. Document Production This document was composed in Microsoft Word and produced in Adobe Professional 9.0. The text font is Microsoft Word Palatino Linotype, and fonts for headings are Microsoft Word Arial. The cover and text papers used in this publication meet the minimum requirements of the Ameri- can National Standard for Permanence of Paper for Printed Library Materials Z39.48—1992. Table of Contents ACKNOWLEDGMENTS ............................................................................................................................................. ii AUTHORS, CONTRIBUTORS, AND TEAM MEMBERS .................................................................................... iii ABSTRACT .................................................................................................................................................................... v EXECUTIVE SUMMARY ........................................................................................................................................... 1 INTRODUCTION ....................................................................................................................................................... 29 How This Report is Organized ................................................................................................................................ 33 Chapter Reports ..................................................................................................................................................... 37 PERDIDO BAY ........................................................................................................................................................... 37 PENSACOLA BAY ..................................................................................................................................................... 43 CHOCTAWHATCHEE BAY ..................................................................................................................................... 56 ST. ANDREW BAY ..................................................................................................................................................... 65 ST. JOSEPH BAY ........................................................................................................................................................ 76 FRANKLIN COUNTY COASTAL WATERS ......................................................................................................... 89 NORTHERN BIG BEND ......................................................................................................................................... 101 SOUTHERN BIG BEND .......................................................................................................................................... 118 SUWANNEE SOUND, CEDAR KEYS, AND WACCASASSA BAY ................................................................ 132 SPRINGS COAST ..................................................................................................................................................... 139 WESTERN PINELLAS COUNTY .......................................................................................................................... 152 TAMPA BAY .............................................................................................................................................................. 158 SARASOTA BAY........................................................................................................................................................ 167 CHARLOTTE HARBOR REGION ......................................................................................................................... 176 ESTERO BAY ............................................................................................................................................................ 190 ROOKERY BAY ........................................................................................................................................................ 201 TEN THOUSAND ISLANDS .................................................................................................................................. 206 FLORIDA KEYS REGION ....................................................................................................................................... 214 FLORIDA BAY .......................................................................................................................................................... 222 BISCAYNE BAY ........................................................................................................................................................ 234 LAKE WORTH LAGOON ....................................................................................................................................... 246 SOUTHERN INDIAN RIVER ................................................................................................................................. 255 NORTHERN INDIAN RIVER ................................................................................................................................ 266 i Acknowledgments This revision of the SIMM report again culminates the collaboration of hundreds of people. Many provided data or wrote chapters for this report, and this revision was not possible without their contributions. Amber Whittle, Crystal York, Sarah Nappier, and Corday Selden reviewed drafts. Bland Crowder copyedited the final text; Jessica Pernell, Jan Boyett, Robin Grunwald, and Dave Reed provided assistance with report production. Others provided and managed grant funds. We continue to be grateful to those who laid the groundwork for the Seagrass Integrated Mapping and Monitoring (SIMM) program and similar efforts to collate, summarize, and share data on seagrasses in Florida’s coastal waters. Efforts in Tampa Bay and the Indian River Lagoon were especially critical in demonstrating the need for regular assessment of seagrass cover, the link between water quality and seagrass abundance, and the effectiveness of seagrass mapping and monitoring in assessing improvements in water quality. Hundreds of scientists and managers participated in those efforts over decades. Regrettably, only the current project participants are listed in the table that follows and in the individual chapters; but they stand, as does the SIMM team, on the shoulders of those who came before. The second edition of FWRI Technical Report 17 was funded by several grants. Support was provided by Florida’s Wildlife Legacy Initiative and the U.S. Fish and Wildlife Service’s State Wildlife Grants program, grants F12AF00071 (FL T-28-R) Targeted