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A Technical Characterization of Estuarine and Coastal New Hampshire New Hampshire Estuaries Project

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A Technical Characterization of Estuarine and Coastal New Hampshire New Hampshire Estuaries Project AR-293 University of New Hampshire University of New Hampshire Scholars' Repository PREP Publications Piscataqua Region Estuaries Partnership 2000 A Technical Characterization of Estuarine and Coastal New Hampshire New Hampshire Estuaries Project Stephen H. Jones University of New Hampshire Follow this and additional works at: http://scholars.unh.edu/prep Part of the Marine Biology Commons Recommended Citation New Hampshire Estuaries Project and Jones, Stephen H., "A Technical Characterization of Estuarine and Coastal New Hampshire" (2000). PREP Publications. Paper 294. http://scholars.unh.edu/prep/294 This Report is brought to you for free and open access by the Piscataqua Region Estuaries Partnership at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in PREP Publications by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. A Technical Characterization of Estuarine and Coastal New Hampshire Published by the New Hampshire Estuaries Project Edited by Dr. Stephen H. Jones Jackson estuarine Laboratory, university of New Hampshire Durham, NH 2000 TABLE OF CONTENTS ACKNOWLEDGEMENTS TABLE OF CONTENTS ............................................................................................i LIST OF TABLES ....................................................................................................vi LIST OF FIGURES.................................................................................................viii PREFACE ..............................................................................................................xii EXECUTIVE SUMMARY........................................................................................xiii CHAPTER 1 INTRODUCTION .........................................................................1 1.1 Geographical and Physical Settings. ..........................................................4 1.1.1 The Great Bay Estuary ..........................................................................4 1.1.2 Hampton Harbor Estuary......................................................................8 1.1.3 Beach and Dune Systems .....................................................................9 1.2 Biological Setting......................................................................................10 1.2.1 Fish and Shellfish................................................................................10 1.2.2 Birds and Mammals............................................................................11 1.2.3 Primary Producers..............................................................................12 1.3 Human Setting..........................................................................................13 1.3.1 Recreational Resources and Values......................................................13 1.3.1.1 Boating ......................................................................................14 1.3.1.2 Shellfishing.................................................................................14 1.3.1.3 Fishing .......................................................................................14 1.3.1.4 Passive Recreation ......................................................................18 1.3.2 Commercial Resources and Values ......................................................19 1.3.2.1 Industry and shipping ................................................................19 1.3.2.2 Fishing .......................................................................................19 1.3.2.3 Tourism and Recreational Industries ...........................................19 CHAPTER 2 PRESENT AND HISTORICAL STATUS AND TRENDS OF WATER QUALITY ............................21 2.1 Overall Water Quality and Use Support...................................................22 2.1.1 Background........................................................................................22 2.1.2 Status and Trends of Overall Water Quality and Use Support .............24 2.2 Status and Trends of Microbial Pathogens and Fecal Indicators ............27 2.2.1 Pathogens, Bacterial Fecal Indicators, and Water Quality Standards....27 2.2.1.1 Spatial Distribution.....................................................................28 Great Bay and Upper Little Bay with the Squamscott/Exeter and Lamprey Rivers .................................28 Oyster and Bellamy rivers and Lower Little Bay ..........................33 Salmon Falls, Cocheco and (Upper) Piscataqua Rivers ................35 Portsmouth and Little Harbors and Lower Piscataqua River ........37 Rye Harbor and Coastline...........................................................38 Hampton Harbor and Tributaries................................................39 2.2.1.2 Temporal Trends ........................................................................40 i 2.2.2 Sources of Fecal-Borne Microorganisms..............................................44 2.2.2.1 Storm-related Runoff..................................................................45 2.2.2.2 Wastewater Treatment Facilities and Combined Sewer Overflows...................................................47 2.2.2.3 Septic Systems...........................................................................50 2.2.2.4 Agricultural Runoff and Other Nonpoint Sources .......................51 2.2.3. Modeling and Dye Studies for Bacterial Fate and Transport................52 2.2.4 Impacts of Fecal-Borne Bacteria on Shellfishing ..................................53 2.2.4.1 Historical Sanitary Assessments of Shellfish-growing Waters .......53 2.2.4.2 Present Conditions.....................................................................57 2.2.5 Impacts of Microbial Contamination ..................................................58 2.2.6 Fecal-Borne Viruses and Historical Studies on Indicators and Pathogens ..........................................................58 2.2.7 Autochthonous Microbial Pathogens ..................................................60 2.3 Toxic Organic and Metal Contaminants ..................................................62 2.3.1 Status and Trends for Contaminants in Water.....................................62 2.3.2 Status and Trends for Contaminated Sediments. ................................63 2.3.3 Sources of Toxic Contaminants...........................................................70 2.3.3.1 Stormwater Runoff.....................................................................70 2.3.3.2 Superfund Sites..........................................................................71 2.3.3.3 Documented Groundwater Pollution Sources.............................73 2.3.3.4 Oil Spills.....................................................................................77 2.3.3.5 Fertilizer and Pesticide Applications............................................78 2.3.3.6 Atmospheric Deposition.............................................................79 2.3.3.7 Summary ...................................................................................79 2.3.4 Contaminant and Hydrodynamic Modelling.......................................80 2.3.5 Public Health Risks and Ecological Impacts. ........................................81 2.4 Inorganic and Organic Nutrients .............................................................87 2.4.1 Nutrient Conditions in New Hampshire’s Estuaries. ............................87 2.4.2 Trends in Nutrient Concentrations......................................................92 2.4.3. Relationship to Water Quality Standards.............................................95 2.4.4 Pollution Sources and Nitrogen Loading Estimates. ............................96 2.4.5 Documented Impacts on Water Chemistry and Natural Resources ...101 2.4.5.1 Dissolved Oxygen....................................................................102 2.4.5.2 Phytoplankton Blooms.............................................................105 2.4.5.3 Eutrophication. ........................................................................107 2.5 Suspended Sediments and Turbidity......................................................109 2.5.1 Surficial Sediments Around Great Bay Estuary ..................................109 2.5.2 Shoreline Characteristics in the Great Bay Estuary ............................109 2.5.3 Sources of Sediments .......................................................................110 2.5.4 Suspended Sediments......................................................................110 2.5.5 Sedimentation Processes on Great Bay Tidal Flats.............................113 2.6 Other Contaminants of Potential Concern ............................................114 2.6.1 Radionuclides ...................................................................................114 2.6.2 Biotoxins ..........................................................................................114 2.6.3 Acid Rain..........................................................................................115 2.6.4 Marine Debris...................................................................................115 2.6.5 Other Contaminants.........................................................................116 2.7 Summary of Findings..............................................................................117 ii CHAPTER 3 LIVING RESOURCES................................................................121 3.1 Estuarine Invertebrates...........................................................................122
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