San Antonio Bay Status and Trends Reports REPORT 1: Water Quality, Benthic Macrofauna, and Epibenthic Fauna REPORT 2: Marine Resources REPORT 3: Colonial Nesting Waterbirds REPORT 4: Whooping Crane REPORT 5: Upland Birds REPORT 6: Attwater’s Prairie Chicken REPORT 7: Aplomado Falcon March 2014 San Antonio Bay: Status and Trends Reports PREPARED BY: Kiersten M. Stanzel, Ph.D. James A. Dodson San Antonio Bay Partnership CONTRIBUTING AUTHORS: Paul Montagna, Ph.D. Terry Palmer Harte Research Institute Tim Anderson Beau Hardegree United States Fish and Wildlife Service Norman Boyd Walter Bubley,Ph.D. Brent Ortego Texas Parks and Wildlife Department Ray Kirkwood Mid‐Coast Chapter, Texas Master Naturalist IN COOPERATION WITH: Coastal Bend Bays & Estuaries Program FUNDING PROVIDED BY: Texas General Land Office, Coastal Management Program, Cycle 16 This paper is funded by a grant/cooperative agreement from the National Oceanic and Atmospheric Administration. The views expressed herein are those of the author(s) and do not necessarily reflect the views of NOAA or any of its sub‐agencies. March 2014 Full document should be cited as: Stanzel, K.M and J.A. Dodson, eds. 2014. San Antonio Bay: Status and Trends Reports. Coastal Bend Bays & Estuaries Program Publication CBBEP‐92. pp. 1‐241. Individual reports should be cited as: Montagna, P.A. and T.A. Palmer. 2014. Report 1: Water Quality, Benthic Macrofauna, dan Epibenthic Fauna (pp. 1‐20). In San Antonio Bay : Status and Trends Reports. Coastal Bend Bays & Estuaries Program Publication CBBEP‐XX. pp. 1‐241. Boyd, N. and W. Bubley. 2014. Report 2: Marine Resources (pp. 1‐167). In San Antonio Bay : Status and Trends Reports. Coastal Bend Bays & Estuaries Program Publication CBBEP‐92. pp. 1‐241. Hardegree, B. 2014. Report 3: Colonial Nesting Water Birds (pp. 1‐33). In San Antonio Bay : Status and Trends Reports. Coastal Bend Bays & Estuaries Program Publication CBBEP‐92. pp. 1‐241. Kirkwood, R. 2014. Report 4: Whooping Crane (pp. 1‐10). In San Antonio Bay : Status and Trends Reports. Coastal Bend Bays & Estuaries Program Publication CBBEP‐92. pp. 1‐241. Ortego, B. 2014. Report 5: Upland Birds (pp. 1‐4). In San Antonio Bay : Status and Trends Reports. Coastal Bend Bays & Estuaries Program Publication CBBEP‐92. pp. 1‐241. Anderson, T. 2014. Report 6: Attwater’s Prairie Chicken (pp. 1‐4). In San Antonio Bay : Status and Trends Reports. Coastal Bend Bays & Estuaries Program Publication CBBEP‐92. pp. 1‐241. Anderson, T. 2014. Report 6: Aplomado Falcon (pp. 1‐3). Inn Sa Antonio Bay : Status and Trends Reports. Coastal Bend Bays & Estuaries Program Publication CBBEP‐92. pp. 1‐241. TABLE OF CONTENTS Executive Summary .......................................................................................................................... i REPORT 1: Water Quality, Benthic Macrofauna, and Epibenthic Fauna ..................................... 1.1 Introduction ......................................................................................................................................... 1.2 Methods ............................................................................................................................................... 1.3 Estuarine Data Acquisition ................................................................................................................. 1.3 Changes in Estuarine Water Quality .................................................................................................. 1.3 Changes in Macrofauna and Epifauna Communities ......................................................................... 1.4 Results .................................................................................................................................................. 1.5 Water Quality ..................................................................................................................................... 1.5 Macrofauna and Epifauna Communities ........................................................................................... 1.5 Discussion .......................................................................................................................................... 1.19 References ......................................................................................................................................... 1.19 REPORT 2: Marine Resources ..................................................................................................... 2.1 Introduction ......................................................................................................................................... 2.2 Fishery Independent Data.................................................................................................................. 2.3 Fishery Dependent Data .................................................................................................................... 2.3 Recreational Harvest Data ............................................................................................................. 2.3 Commercial Harvest Data .............................................................................................................. 2.4 Assemblage Data ............................................................................................................................... 2.4 Spatial Distribution of Species ........................................................................................................... 2.4 Species Diversity ................................................................................................................................ 2.4 Methods ............................................................................................................................................... 2.5 Fishery Independent Data.................................................................................................................. 2.5 Fishery Dependent Data .................................................................................................................... 2.6 Recreational Harvest Data ............................................................................................................. 2.6 Commercial Harvest Data .............................................................................................................. 2.6 Assemblage Data ............................................................................................................................... 2.6 Spatial Distribution of Species ........................................................................................................... 2.7 Species Diversity ................................................................................................................................ 2.8 Results .................................................................................................................................................. 2.9 Fishery Independent Data.................................................................................................................. 2.9 Fishery Dependent Data .................................................................................................................. 2.59 Recreational Harvest .................................................................................................................... 2.59 Commercial Harvest ..................................................................................................................... 2.73 Assemblage Data ............................................................................................................................. 2.88 Annual Species Assemblages within SAB ................................................................................... 2.105 Spatial Distribution of Species ....................................................................................................... 2.108 Bag Seine .................................................................................................................................... 2.108 Bay Trawl .................................................................................................................................... 2.128 Gillnet ......................................................................................................................................... 2.143 Species Diversity ............................................................................................................................ 2.163 Discussion ........................................................................................................................................ 2.166 Non‐native species ......................................................................................................................... 2.166 Future Threats/Considerations ...................................................................................................... 2.167 References ....................................................................................................................................... 2.167 REPORT 3: Colonial Nesting Waterbirds ..................................................................................... 3.1 Introduction ......................................................................................................................................... 3.2 Methods ..............................................................................................................................................