The Ecology of the South Slough Estuary: Site Profile of the South Slough National Estuarine Research Reserve Steven S. Rumrill South Slough National Estuarine Research Reserve Charleston, Oregon The Ecology of the South Slough Estuary: Site Profile of the South Slough National Estuarine Research Reserve, Oregon Steven S. Rumrill South Slough National Estuarine Research Reserve Charleston, Oregon The Ecology of the South Slough Estuary: Site Profile of the South Slough National Estuarine Research Reserve The Ecology of the South Slough Estuary: Site Profile of the South Slough National Estuarine Research Reserve THE ECOLOGY OF THE SOUTH SLOUGH ESTUARY, OREGON: SITE PROFILE OF A NATIONAL ESTUARINE RESEARCH RESERVE Steven S. Rumrill South Slough National Estuarine Research Reserve TABLE OF CONTENTS ..................................................................................... i LIST OF FIGURES ............................................................................................... iv LIST OF TABLES ................................................................................................. x ACKNOWLEDGEMENTS .................................................................................. xii PREFACE ................................................................................................................. xiii CHAPTER 1. INTRODUCTION TO THE SOUTH SLOUGH ESTUARY 1.1 Coastal Components of the Lower Columbia Bioregion .................................. 1 1.1.1 Geological Setting ....................................................................................... 4 1.1.2 Coastal Climate, Ocean Currents and Upwelling ........................................ 6 1.1.3 Diversity of Habitats and Biotic Communities............................................ 10 1.2 Estuaries in the Lower Columbia Bioregion ...................................................... 14 1.2.1 Definition and Classification of Estuaries.................................................... 14 1.2.2 Regional Estuarine Management Concerns ................................................. 16 1.3 Coos Watershed and Estuary .............................................................................. 18 1.3.1 Physical Description of the Coos Estuary .................................................... 19 1.3.2 Biotic Resources of the Coos Estuary .......................................................... 24 1.4 South Slough Watershed and the South Slough National Estuarine Research Reserve ....................................................................... 27 1.4.1 South Slough Watershed and Estuary .......................................................... 27 1.4.2 Recognition and Designation as a National Estuarine Research Reserve...... 30 1.4.3 South Slough National Estuarine Research Reserve ..................................... 32 CHAPTER 2. GEOLOGICAL FRAMEWORK AND ENVIRONMENTAL SETTING 2.1 Coastal Geology within the Charleston Quadrangle......................................... 37 2.1.1 Coastal Tectonic Setting .............................................................................. 37 2.1.2 Geologic History of the South Slough Watershed ....................................... 37 2.1.3 Quaternary Geologic History ...................................................................... 42 2.1.4 Formation of Buried Peat Layers ................................................................. 43 2.1.5 Geomorphology of the South Slough Tidal Inlet ......................................... 45 2.1.6 Recent Alterations to the Geomorphology of the Tidal Channels................ 48 2.2 Regional and Local Climate Conditions ............................................................ 48 2.2.1 Seasonal Temperature, Precipitation, and Wind Patterns ............................. 48 2.2.2 Pulsed Storm Events .................................................................................... 49 2.3 Soils in the South Slough Watershed.................................................................. 50 2.3.1 Soils in Upland Forested Areas .................................................................... 51 2.3.2 Riparian Areas, Wetlands, and Saltmarshes.................................................. 52 2.3.3 Tideflats and Sandflats ................................................................................ 52 2.3.4 Subtidal Channel Sediments ....................................................................... 55 i The Ecology of the South Slough Estuary: Site Profile of the South Slough National Estuarine Research Reserve 2.4 Hydrology of the South Slough Watershed ........................................................ 55 2.4.1 Principal Streams and Freshwater Inputs ..................................................... 55 2.4.2 Tidal Dynamics and Circulation Patterns.................................................... 59 2.5 Physiochemical Characteristics of the South Slough Estuary ........................... 64 2.5.1 Temperature and Salinity Cycles ................................................................. 64 2.5.2 Dissolved Oxygen and pH levels ................................................................. 68 2.5.3 Nutrients, Turbidity, and Dissolved Solids .................................................. 68 2.5.4 Water Quality within the South Slough Estuary.......................................... 70 2.5.5 Sediment Contaminants.............................................................................. 73 2.6 Accretion of Sediments in the South Slough Estuary ........................................ 74 2.7 Watershed Land Use and Ownership ................................................................. 74 CHAPTER 3. ESTUARINE HABITATS AND COMMUNITIES 3.1 Habitat Classification Scheme within the South Slough Estuary ..................... 77 3.2 Open Water and the Estuarine Water Column .................................................. 78 3.2.1 Estuarine Phytoplankton and Protist Communities .................................... 78 3.2.2 Neustonic Layer .......................................................................................... 82 3.2.3 Zooplankton Communities ......................................................................... 83 3.2.4 Nekton and Midwater Fish ......................................................................... 86 3.3 Tidal Channels and Subtidal Habitat................................................................. 91 3.3.1 Subtidal Macroalgae .................................................................................... 92 3.3.2 Subtidal and Sublittoral Invertebrates.......................................................... 92 3.3.3 Resident and Migratory Fish ....................................................................... 98 3.4 Sandflat and Mudflat Habitats ........................................................................... 105 3.4.1 Benthic Microphyton Communities and the Redox Potential Discontinuity 105 3.4.2 Eelgrass Communities ................................................................................. 109 3.4.3 Macrobenthic Algae and Seaweed Communities ......................................... 114 3.4.4 Meiofauna and Infaunal Invertebrates ......................................................... 116 3.4.5 Epibenthic Invertebrates.............................................................................. 133 3.5 Ecological Interactions within Estuarine Communities.................................... 133 3.5.1 Interspecific Interactions among Pacific Ghost Shrimp, Infaunal Invertebrates, and Predatory Sculpins.......................................................... 133 3.5.2 Alteration of Eelgrass Community Structure by Mariculture of Pacific Oysters .... 135 3.5.3 Regrowth and Recovery of Eelgrass Communities ....................................... 137 3.5.4 Diet and Ecological Role of Cutthroat Trout in Estuarine Tidal Channels .. 140 3.6 Introduction and Spread of Non-Indigenous Species........................................ 141 3.6.1 Extent of Estuarine Invasions by Non-Indigenous Aquatic Species.............. 141 3.6.2 Colonization of Tideflats by European Green Crabs.................................... 145 3.6.3 Spread and Community Alteration by Japanese Eelgrass ............................. 145 3.6.4 Future Management of Non-Indigenous Species in the South Slough Estuary .. 148 3.7 Emergent Saltmarshes ......................................................................................... 149 3.7.1 Geomorphology of South Slough Salt Marshes ........................................... 149 3.7.2 Emergent Salt Marsh Vegetation Communities ........................................... 150 3.7.3 Salt Marsh Invertebrates .............................................................................. 153 3.7.4 Ecological Importance of Salt Marshes ........................................................ 154 3.8 Hard Substrata and Anthropogenic Habitats .................................................... 155 3.9 Migratory Birds and Waterfowl .......................................................................... 158 3.10 Use of Estuarine Habitats by Mammals ............................................................. 159 ii The Ecology of the South Slough Estuary: Site Profile of the South Slough National Estuarine Research Reserve CHAPTER 4. RIPARIAN COMMUNITIES AND UPLAND HABITATS 4.1 Riparian Habitats and Upland Forests in the Oregon Coast Range ................. 163 4.2 Riparian Habitats and Communities