Peer Review (Independent Technical Review) of the Massachusetts Estuaries Project Report on the Pleasant Bay System DRAFT REPORT April 2009 Prepared for: George Meservey, Director of Planning and Community Development Town of Orleans 19 School Road Orleans, MA 02653 Woods Hole Group, Inc. Table of Contents EXECUTIVE SUMMARY ........................................................................................ ES-1 E.1 PURPOSE/EXPECTATIONS FOR THIS DRAFT REPORT ........................................... ES-2 E.2 OVERALL SUMMARY OF THE INDEPENDENT TECHNICAL REVIEW ....................... ES-6 E.3 TASK 1 BENTHIC FLUX REVIEW ......................................................................... ES-7 E.4 TASK 2 HYDRODYNAMIC AND WATER QUALITY MODELING REVIEW ................. ES-9 E.5 TASK 3 EELGRASS AND BENTHIC COMMUNITY REVIEW ................................... ES-12 E.6 RECOMMENDED NEXT STEPS ........................................................................... ES-13 1.0 BENTHIC FLUX MEASUREMENTS AND ANALYSIS OF MECHANISMS................................................................................................................. 1 1.1 INTRODUCTION ....................................................................................................... 1 1.2 OVERALL COMMENT ............................................................................................... 2 1.3 SEDIMENT NITROGEN CYCLING: BIOGEOCHEMICAL BASICS .................................... 3 1.4 EVALUATION OF TECHNICAL APPROACH ................................................................. 5 1.4.1 Sampling Design ......................................................................................... 5 1.4.2 Evaluation of Flux Data .............................................................................. 7 1.4.3 Benthic Flux Modeling ............................................................................... 9 1.4.4 Effects on Bottom Water Oxygen ............................................................... 9 1.5 COMPARATIVE DATA ............................................................................................. 10 1.6 IMPLICATIONS ....................................................................................................... 10 1.7 RESPONSE TO SELECT COMMITTEE COMMENTS ...................................................... 11 1.7.1 Chapter IV Comments .............................................................................. 11 1.7.2 Chapter VIII Comments ............................................................................ 13 2.0 HYDRODYNAMIC AND WATER QUALITY MODELING ..................... 19 2.1 INTRODUCTION ..................................................................................................... 19 2.2 HYDRODYNAMIC MODELING ................................................................................. 20 2.2.1 Key Comments .......................................................................................... 20 2.2.1.1 Influence of Potential Stratification Effects ........................................ 20 2.2.1.2 Tidal Attenuation in Upper Subembayments ...................................... 24 2.2.1.3 Simulation of Anthropogenic Structures ............................................ 25 2.2.1.4 Tidal Residual ..................................................................................... 26 DRAFT REPORT - Peer Review (Independent Technical Review) April 2009 of the Massachusetts Estuaries Project Report Town of Orleans, MA on the Pleasant Bay System 2009-002 i Woods Hole Group, Inc. 2.2.2 Minor Comments ...................................................................................... 28 2.2.2.1 Data Collection and Analysis.............................................................. 28 2.2.2.2 Hydrodynamic Modeling .................................................................... 29 2.2.2.3 General Comments .............................................................................. 30 2.2.3 Response to WMVDC Comments ............................................................ 31 2.3 WATER QUALITY MODELING ................................................................................. 35 2.3.1 Key Comments .......................................................................................... 35 2.3.1.1 Water Quality Boundary Conditions (Bioactive vs. Total Nitrogen) . 35 2.3.1.2 Selection and Sensitivity of Dispersion Coefficients .......................... 36 2.3.1.3 Calibration and Verification of RMA-4 .............................................. 37 2.3.1.4 Mass Conservation in RMA-4 ............................................................ 38 2.3.1.5 RMA-4 Model Selection ..................................................................... 38 2.3.1.6 Background Nitrogen Concentration Level ........................................ 39 2.3.2 Minor Comments ...................................................................................... 39 2.3.3 Response to WMVDC Comments ............................................................ 40 2.4 IMPACTS TO INLET MIGRATION AND BREACHES COMMENTS .................................. 44 2.4.1 Key Comments .......................................................................................... 44 2.4.2 Minor Comments ...................................................................................... 45 2.4.3 Response to WMVDC Comments ............................................................ 45 2.5 ADDITIONAL OVERALL COMMENTS ....................................................................... 46 3.0 HEALTH OF EELGRASS AND BENTHIC COMMUNITY ...................... 49 3.1 OXYGEN AND NITROGEN IN THE WATER COLUMN .................................................. 49 3.2 BOTTOM OXYGEN AND BENTHIC POPULATIONS ..................................................... 49 3.3 EELGRASS DISTRIBUTION ...................................................................................... 52 3.4 BIOACTIVE NITROGEN ........................................................................................... 53 3.5 BOATING ACTIVITY ............................................................................................... 53 3.6 RECOVERY TIME .................................................................................................... 54 3.7 RESPONSE TO VALIDATION COMMITTEE COMMENTS ............................................. 54 APPENDIX A BIO SKETCHES ........................................................................... A-1 APPENDIX B RESUMES ..................................................................................... B-1 DRAFT REPORT - Peer Review (Independent Technical Review) April 2009 of the Massachusetts Estuaries Project Report Town of Orleans, MA on the Pleasant Bay System 2009-002 ii Woods Hole Group, Inc. List of Figures Figure 1. Simplified sediment nitrogen cycle (Cornwell et al. 1999). The conversion of PON to DON and finally to NH4+ is variously called remineralization or ammification. Fluxes across the sediment-water interface are driven by + concentration differences across that boundary; sediment NH4 concentrations can be orders of magnitude higher than water column concentrations. The backwards arrow from nitrate to ammonium is referred to dissimilatory nitrate reduction to ammonium (DNRA) and often occurs in sulfidic sediments. ........4 Figure 2. Depth-averaged temperature and salinity at the deepest part of Arey’s Pond in 2001. Observations from Horne and Horne (2001). .......................................21 Figure 3. Vertical gradients of temperature and salinity at the deepest part of Arey’s Pond. Error bars represent 95% confidence limits..........................................22 Figure 4. Depth-averaged vertical squared buoyancy frequency at the deepest part of Arey’s Pond. Error bars represent 95% confidence limits. .............................23 Figure 5. Surface and bottom concentrations of dissolved oxygen at the deepest part of Arey’s Pond. ....................................................................................................25 Figure 6. Barometric pressure, wind speed and direction, and precipitation observations during the 43 day tidal deployment period presented in the MEP Pleasant Bay report. Data collected by NOAA’s National Climactic Data Center at Chatham Municipal Airport. ............................................................................28 Figure 7 Affect of nitrogen on algal growth. ..................................................................51 List of Tables Table 1. Rates of sediment N regeneration in Pleasant Bay. ...........................................8 Table 2. Loading and benthic flux rates: whole system from report tables VI-2, VI-6, and VI.2.6.2........................................................................................................9 Table 3. Manning’s n Values for Culverts (Norman et al., 2001). ................................27 DRAFT REPORT - Peer Review (Independent Technical Review) April 2009 of the Massachusetts Estuaries Project Report Town of Orleans, MA on the Pleasant Bay System 2009-002 iii Woods Hole Group, Inc. EXECUTIVE SUMMARY This report presents the Draft results of an independent technical review (peer review) conducted on the Massachusetts Estuaries Project Report for the Pleasant Bay System in the Town of Orleans. This work was conducted under a contract to the Town of Orleans, which was awarded to the Woods Hole Group after a competitive Request for Proposal