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Massachusetts Estuaries Project Massachusetts Estuaries Project Linked Watershed-Embayment Model to Determine Critical Nitrogen Loading Thresholds for Three Bays, Barnstable, Massachusetts University of Massachusetts Dartmouth Massachusetts Department of School of Marine Science and Technology Environmental Protection FINAL REPORT –APRIL 2006 Massachusetts Estuaries Project LINKED WATERSHED-EMBAYMENT MODEL TO DETERMINE CRITICAL NITROGEN LOADING THRESHOLDS FOR THREE BAYS IN THE TOWN OF BARNSTABLE, MA FINAL REPORT – APRIL 2006 Brian Howes Roland Samimy David Schlezinger Sean Kelley John Ramsey Ed Eichner Contributors: US Geological Survey Don Walters and John Masterson Applied Coastal Research and Engineering, Inc. Elizabeth Hunt and Jessica Cote Massachusetts Department of Environmental Protection Charles Costello and Brian Dudley (DEP project manager) SMAST Coastal Systems Program George Hampson, Sara Sampieri, Elizabeth White Cape Cod Commission Vanessa Puchi and Maisy McDarby-Stanovich © [2006] University of Massachusetts All Rights Reserved ACKNOWLEDGMENTS The Massachusetts Estuaries Project Technical Team would like to acknowledge the contributions of the many individuals who have worked tirelessly for the restoration and protection of the critical coastal resources of the Three Bays System. Without these stewards and their efforts, this project would not have been possible. First and foremost we would like to recognize and applaud the significant time and effort in data collection and discussion spent by members of the Three Bays Water Quality Monitoring Program and SMAST “volunteers”. These individuals gave of their time to collect nutrient samples from this system, without which the present analysis would not have been possible. Of particular note are Lindsey Counsell of Three Bays Preservation, Coordinator of the Monitoring Program, and John Jacobsen of the Town of Barnstable, Coordinator of the Town- wide Monitoring Program. Similarly, many in the Town of Barnstable helped in this effort, the Barnstable Department of Public Works and the Barnstable Shellfish Department, as well as the Barnstable Nutrient Management Committee. The technical team would like to specifically acknowledge the efforts of Mark Ells for helping to move this effort forward and Three Bays Preservation for their energy and perseverance in the stewardship of one of the regions key coastal resources. In addition to local contributions, technical, policy and regulatory support has been freely and graciously provided by Tom Camberari and Margo Fenn of the Cape Cod Commission; Art Clark and Nora Conlon of the USEPA; and our MADEP colleagues: Andrew Gottlieb, Arleen O’Donnell, Art Screpetis, Rick Dunn, Steve Halterman, Russ Issac, Glenn Haas, and Ron Lyberger. We are also thankful for the long hours in the field and laboratory spent by the many technical staff (Jennifer Antosca, Michael Bartlett, and David White), interns and students within the Coastal Systems Program at SMAST-UMD. Support for this project was provided by the Town of Barnstable, Barnstable County, MADEP, and the USEPA, with in-kind support from Three Bays Preservation Inc. CITATION Howes B., S. W. Kelley, J. S. Ramsey, R. Samimy, D. Schlezinger, E. Eichner (2006). Linked Watershed-Embayment Model to Determine Critical Nitrogen Loading Thresholds for Three Bays, Barnstable, Massachusetts. Massachusetts Estuaries Project, Massachusetts Department of Environmental Protection. Boston, MA. © [2006] University of Massachusetts All Rights Reserved MASSACHUSETTS ESTUARIES PROJECT TABLE OF CONTENTS I. INTRODUCTION ......................................................................................................................1 I.1 THE MASSACHUSETTS ESTUARIES PROJECT APPROACH ........................................4 I.2 SITE DESCRIPTION...........................................................................................................7 I.3 NUTRIENT LOADING .......................................................................................................12 I.4 WATER QUALITY MODELING.........................................................................................14 I.5 REPORT DESCRIPTION..................................................................................................15 II. PREVIOUS STUDIES RELATED TO NITROGEN MANAGEMENT.....................................16 III. DELINEATION OF WATERSHEDS .....................................................................................19 III.1 BACKGROUND...............................................................................................................19 III.2 MODEL DESCRIPTION ..................................................................................................19 III.3 THREE BAYS CONTRIBUTORY AREAS.......................................................................20 IV. WATERSHED NITROGEN LOADING TO EMBAYMENT: LAND USE, STREAM INPUTS, AND SEDIMENT NITROGEN RECYCLING ........................................................26 IV.1 WATERSHED LAND USE BASED NITROGEN LOADING ANALYSIS .........................26 IV.1.1 Land Use and Water Use Database Preparation.....................................................29 IV.1.2 Nitrogen Loading Input Factors................................................................................32 IV.1.3 Calculating Nitrogen Loads ......................................................................................37 IV.2 ATTENUATION OF NITROGEN IN SURFACE WATER TRANSPORT.........................46 IV.2.1 Background and Purpose.........................................................................................46 IV.2.2 Surface Water Discharge and Attenuation of Watershed Nitrogen: Marstons Mills River to Warren’s Cove/Prince’s’s Cove (head of North Bay) .........................49 IV.2.3 Freshwater Discharge and Attenuation of Watershed Nitrogen: Little River to Cotuit Bay ................................................................................................................53 IV.3 BENTHIC REGENERATION OF NITROGEN IN BOTTOM SEDIMENTS......................57 IV.3.1 Sediment-Watercolumn Exchange of Nitrogen ........................................................57 IV.3.2 Method for Determining Sediment-Watercolumn Nitrogen Exchange......................58 IV.3.3 Rates of Summer Nitrogen Regeneration from Sediments ......................................60 V. HYDRODYNAMIC MODELING ............................................................................................64 V.1 INTRODUCTION..............................................................................................................64 V.2 GEOMORPHIC AND ANTHROPOGENIC EFFECTS TO THE ESTUARINE SYSTEM..66 V.2.1 Natural Coastal Processes.........................................................................................66 V.2.2 Anthropogenic Changes Influencing Rushy Marsh Pond...........................................68 V.3 DATA COLLECTION AND ANALYSIS ............................................................................72 V.3.1 Bathymetry Data Collection.......................................................................................72 V.3.2 Tide Data Collection and Analysis.............................................................................73 V.3.3 ADCP Data Analysis .................................................................................................82 V.4 HYDRODYNAMIC MODELING .......................................................................................93 V.4.1 Model Theory ............................................................................................................93 V.4.2 Model Setup ..............................................................................................................93 V.4.2.1 Grid generation ...................................................................................................94 V.4.2.2 Boundary condition specification ........................................................................94 V.4.2.3 Calibration...........................................................................................................96 V.4.2.3.1 Friction coefficients ..........................................................................................96 V.4.2.3.2 Turbulent exchange coefficients ......................................................................97 V.4.2.3.3 Wetting and Drying ..........................................................................................97 i MASSACHUSETTS ESTUARIES PROJECT V.4.2.3.4 Comparison of modeled tides and measured tide data ...................................97 V.4.2.4 Model Verification .............................................................................................102 V.4.2.5 ADCP verification of the Three Bays system....................................................103 V.4.2.6 Model Circulation Characteristics .....................................................................107 V.5 FLUSHING CHARACTERISTICS..................................................................................112 VI. WATER QUALITY MODELING ..........................................................................................116 VI.1 DATA SOURCES FOR THE MODEL ...........................................................................116 VI.1.1 Hydrodynamics and Tidal Flushing in the Embayments ........................................116 VI.1.2 Nitrogen Loading to the Embayments ....................................................................116 VI.1.3
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