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University of New Hampshire University of New Hampshire Scholars' Repository Institute for the Study of Earth, Oceans, and Space PREP Reports & Publications (EOS) 10-10-1992 The ecology of the Great Bay Estuary, New Hampshire and Maine: An Estuarine Profile and Bibliography Frederick T. Short The Jackson Laboratory, [email protected] Follow this and additional works at: https://scholars.unh.edu/prep Recommended Citation Short, Frederick T., "The ce ology of the Great Bay Estuary, New Hampshire and Maine: An Estuarine Profile and Bibliography" (1992). PREP Reports & Publications. 376. https://scholars.unh.edu/prep/376 This Report is brought to you for free and open access by the Institute for the Study of Earth, Oceans, and Space (EOS) at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in PREP Reports & Publications by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. THE ECOLOGY OF THE GREAT BAY ESTUARY, NEW HAMPSHIRE AND MAINE: AN ESTUARINE PROFILE AND BIBLIOGRAPHY ~ Edited by Fredrick T. Short NOAA .bo Ne>\ ~/)/ovE: ESTUARINE RESERVES DIVISION University of Ne\'\r Hampshire 1305 Jackson Estuarine Laboratory EAST-WEST HIGHWAY N/ORMc SILVER SPRINGS, MD 20910 ' Durham, New Hampshire • This volume is dedicated to Dr. Galen E. Jones, former Director of the Jackson Estuarine Laboratory and retired Professor of Microbiology at the University of New Hampshire. Galen is a great supporter of marine and estuarine research and worked for years to establish the strong marine research program at the University of New Hampshire. Cover Photograph is an aerial view of the Great Bay Estuary, with Dover Point and the Piscataqua River in the foreground, looking across Little Bay to Great Bay. Drawings by Victor E. Young and Funi Burdick. Photographs by Fredrick T. Short The Ecology of The Great Bay Estuary, New Hampshire and Maine: An Estuarine Profile al')d Bibliography Edited by Frederick T. Short Jackson Estuarine Laboratory University of New Hampshire Durham, New Hampshire October 1992 - The Ecology of the Great Bay Estuary, New Hampshire and Maine: An Es~arine Profile and Bibliography Prepared for: The U.S. Navy through U.S. Environmental Protection Agency, Environmental Research Laboratory, Narragansett, RI. The Great Bay National Estuarine Research Reserve, a program of the New Hampshire Fish and Game Department and the National Oceanic and Atmospheric Administration (NOAA), grant # NA89AA-D-CZ101. Publication of this document made possible by a grant (NA90AA-D-SG458) from NOAA Coastal Ocean Program through the Sea Grant College Program and the University of New Hampshire through the Jackson Estuarine Laboratory. The views expressed herein are those of the authors and do not necessarily reflect the views of the U.S. Navy, NOAA, New Hampshire Fish and Game Department, the University of New Hampshire, or any of their sub-agencies. Jackson Estuarine Laboratory contribution number 264. Copies of this report can be obtained for $10.00 from: The Great Bay National Estuarine Research Reserve New Hampshire Fish and Game 37 Concord Road Durham, NH 03824 This document should be cited as: Short, F.T. 1992. (ed.) The Ecology of the Great Bay Estuary, New Hampshire and Maine: An Estuarine Profile and Bibliography. NOAA - Coastal Ocean Program Publ. 222 pp. i The following authors contributed to The Ecology of The Great Bay Estuary, New Hampshire and Maine: An Estuarine Profile and Bibliography: Dr. Frederick Short (editor) is a research scientist at the Jackson Estuarine Laboratory (JEL) at the University of New Hampshire. He has worked in seagrass research for 18 years and has worked extensively on eelgrass populations in the Great Bay Estuary and all along the East Coast of the US. His recent activities include investigation of numerous aspects of the eelgrass habitat and their effects on estuarine systems. Dr. Stephen Jones, at JEL, conducts research on the fate of pathogenic microorganisms, both fecal-born and indigenous, in estuaries. His work includes factors affecting the sanitary quality of shellfish, the fate of point and nonpoint source fecal pollution, and the ecology of microbial pathogens. Dr. Richard Langan is Manager at Jackson Estuarine Laboratory and has conducted the JEL Water Quality Monitoring Program in the Great Bay Estuary since 1988. He has seven years experience in commercial and experimental shellfish culture, Dr. Arthur Mathieson, at JEL, is a well known phycologist. He has made extensive investigations of macroalgae along the ·northern New England Coast, and particularly in the Great Bay Estuary. Currently he is investigating reproductive allocation strategies, epiphytes, and the evolutionary history of fucoid algae. Dr. Peter Sale is a fish ecologist with experience in the fish habitats of the Great Bay Estuary. He is Director of the Jackson Estuarine Laboratory and Center for Marine Biology. Dr. Larry Ward, at JEL, has extensive experience in studies concerning Holocene sedimentation with emphasis on estuarine and coastal systems. He has worked in various environments along the East Coast of the United States. Mr. Jeff Guy is a research technician who worked for Dr. Sale; he has experience in field research on fish habitats. Ms. Monica Webster, a former UNH graduate student at JEL, is now a biologist at US Army Corps of Engineers. She has a Master's degree in Earth Science and conducted · research on the Adams Point mud flat. Mr. Peter Wellenberger is the Manager of the Great Bay National Estuarine Research Reserve working within the NH Fish and Game Department. He has a Masters degree in Resource Management from Antioch/New England and has extensive experience in dealing with management issues. ii Preface The preparation of The Ecology of The Great Bay Estuary, New Hampshire and Maine: An Estuarine Profile and Bibliography has been a combined effort involving many individuals and agencies. For all those involved, creating the Profile represented an opportunity to pull together the many sources of information concerning the Great Bay Estuary. Many of these sources were scientific, but we have supplemented the science with history, natural history, and social and political information. All of these approaches are valid frames of reference when considering the Estuary, its past, present, and future. We have written the Estuarine Profile as a document to be read and understood by the concerned citizen, by monitoring groups and management agency personnel, as well as by scientists studying this or another estuarine system. Some of the material referenced is of course very technical, but the Profile itself should give an overview of the ecology of the Great Bay Estuary to anyone with the interest to read it. While the Profile may seem lengthy, and indeed we attempted to be thorough, one of the aims of the Profile is to outline what is not yet known about the Great Bay Estuary. If the Profile has a bias beyond completeness of information, it is toward the long­ term preservation of the Estuary as a natural resource for New Hampshire and Maine. Therefore, we set out management priorities for the Estuary, based on the scientific information available. And where information is lacking, we outline the research needed so that science can contribute to decision making about management issues within the Estuary in the future. Direct funding for the project came from the U.S. Department of the Navy through the U.S. Environmental Protection Agency; from the National Estuarine Research Reserve Program, Sanctuaries and Reserves Division, NOAA, U.S. Department of Commerce, through the New Hampshire Fish and Game Department; and from the University of New Hampshire. Because of the magnitude of the project and the overlap with other ongoing research, some sections of the Estuarine Profile and its publication costs were funded under a separate grant from NOAA's Coastal Ocean Program. The information presented in this document combines material from a profile of Great Bay prepared for New Hampshire Fish and Game Department (Short 1991) and a historical overview of the Great Bay Estuary prepared for the U.S. Navy (Short 1992). Some of the background material useci in the document was obtained from the Great Bay Estuarine Research Reserve Management Plan (NHOSP 1989). The Bibliography presented here is updated from the original Research Bibliography of the Great Bay Estuary (Short and Tracy 1986) and the more recent Sea Grant publication (Penniman et al. 1989). The Editor would like to thank all the contributing authors for their cooperation and comments on the entire document. Additionally, thanks to Heather Talbot for her patience and dedication in typing the manuscript, to Allison Currie and Sandy Weiss for research assistance on several chapters, to my wife Cathy Short for excellent suggestions and editing of the final document, and to John Nelson, Robert Croker, Linda Dietz, Jim Tayon, Kristin Wall, and Robert Johnston for their careful reviews of the manuscript. iii TABLE OF CONTENTS Page Preface iii List of Figures vi List of Tables ix Estuarine Profile of the Great Bay Estuary, New Hampshire and Maine 1 Introduction 1 Chapter 1. History of Human Activities and Today's Resource Values in the 5 Great Bay Estuary (Short and Webster) Today's Scenic Resource Values 16 Today's Recreational Resource Values 16 Today's Commercial Resources Values 23 Chapter 2. Characterization of Estuarine Habitats (Short, Sale and Guy) 25 Eelgrass Habitat 25 Mudflat Habitat 28 Salt Marsh Habitat 28 Channel Bottom and Subtidal Habitat 30 Rocky Intertidal Habitat 30 Chapter 3. The Estuarine Hydrosystern (Short) 31 The Watershed 31 Tidal Conditions 33 Chapter 4. Estuarine Geomorphology (Ward) 39 Geology 39 Estuarine Geomorphology and Sedimentary Processes 41 Chapter 5. Estuarine Hydrochemistry (Short) 45 Temperature Environment 45 Salinity Regime 47 Dissolved Oxygen 47 Suspended Load 47 Nutrient Characterization 49 ~ ~ Chapter 6.

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