End Notes

1. See Mallin et al. (2000)

2. See Brabec et al. (2002)

3. See NH Department of Business and Economic Affairs (2021)

4. See U.S. EPA (2009)

5. See UNH Stormwater Center and Vanasse Hangen Brustlin, Inc. (2015)

6. See NHDES (2022)

7. Title 38, §420-D

8. See SWA (2012)

9. See U.S. EPA Office of Wastewater Management (2015)

10. See NHDES (2020)

11. See Western Kentucky University (2021)

12. See PREP (2010)

13. See Wasson et al. (2019)

14. See Anderson and Barnett (2017)

15. See Payne et al. (2019)

16. See Burdick et al. (2020)

17. See Steckler and Ormiston (2021)

18. See Anderson et al. (2020)

19. See ME Department of Inland Fisheries and Wildlife (2017)

20. See NH Fish and Game Department (2020a)

21. See NH Fish and Game Department (2020b)

22. See Steckler and Brickner-Wood (2019)

23. See Steckler et al. (2016)

24. See Zankel et al. (2006)

25. See Walker et al. (2010)

26. See Jones et al. (1992)

27. See Jones (2000)

28. See Lemcke-Stampone et al. (2022)

29. See Jayhoe et al. (2007)

30. See Runkel et al. (2004)

31. See U.S. EPA (2012)

32. See Bricker et al. (2003)

33. See Batiuk et al. (2009)

34. See Morrell and Gobler (2020)

35. See Batiuk et al. (2009)

36. See Barker (2019)

37. See Jones (2000)

38. See Short et al. (1993)

39. See Moore et al. (2014)

40. See U.S. EPA (2012)

41. See Kemp (2004)

42. See Trowbridge (2009)

43. See Bierman (2014)

44. See NH Estuaries Project and Jones (2000)

45. See Jones (2021)

46. See Urquhart et al. (2016)

47. See Xu et al. (2015)

48. See Hartwick et al. (2021)

49. See Ao et al. (2017)

50. See Grizzle and Ward (2020)

51. See Odell et al. (2006)

52. See Stasse et al. (2021)

53. See NH Fish and Game Department (2013)

54. See Grizzle et al. (2021)

55. See Capone et al. (2008)

56. See Grizzle et al. (2021)

57. See Atwood and Grizzle (2020)

58. See Glenn (2016)

59. See Glenn et al. (2020)

60. See Metzger et al. (2015)

61. See Metzger et al. (2016)

62. See Metzger et al. (2018)

63. See Carballal et al. (2015)

64. See Geoghegan et al. (2021)

65. See Normandeau (2021)

66. See NHDES (2017)

67. See Canadian Council of Ministries of the Environment (2023)

68. See Apeti et al. (2021)

69. See NHDES (2021)

70. See Weeks et al. (2011)

71. See Apeti et al. (2021)

72. See Barley-Greenfield (2017)

References

Anderson MG, Barnett A, Clark M, Sheldon AO, Prince J, Vickery B. 2020. Resilient and Connected Landscapes for Terrestrial Conservation, New England version. Boston, MA. The Nature Conservancy, Eastern Conservation Science
Anderson, M.G. and Barnett, A. 2017. Resilient Coastal Sites for Conservation in the Northeast and Mid-Atlantic US. The Nature Conservancy, Eastern Conservation Science.
Ao, Yaping; Goblick, Gregory N.; Calci, Kevin R.; and Nash, William C., “Hydrographic Study of Peirce Island Wastewater Treatment Plant Effluent in the Piscataqua River of Portsmouth, New Hampshire: Report of Findings from the December 10 – 14, 2012 Study Period” (2017). PREP Publications. 372. http://scholars.unh.edu/prep/372  
Apeti, DA, M Rider, S Jones, E Wirth, S Regan. 2021. An Assessment of Contaminants of Emerging Concern in the Gulf of Maine. NOAA Technical Memorandum NOS NCCOS 291. Silver Springs, MD. 118 pp. DOI 10.25923/c2z4-k112.
Apeti, DA, M Rider, S Jones, E Wirth, S Regan. 2021. An Assessment of Contaminants of Emerging Concern in the Gulf of Maine. NOAA Technical Memorandum NOS NCCOS 291. Silver Springs, MD. 118 pp. DOI 10.25923/c2z4-k112.
Atwood, R.L. and R.E. Grizzle (2020) “Eastern Oyster Recruitment Patterns on and Near Natural Reefs: Implications for the Design of Oyster Reef Restoration Projects,” Journal of Shellfish Research 39(2), 283-289. 
Barker, Seth, “Eelgrass Distribution in the Great Bay Estuary and Piscataqua River for 2019: Final Project Report submitted to the Piscataqua Region Estuaries Partnership” (2020). PREP Reports & Publications. 438. https://scholars.unh.edu/prep/438
Barley-Greenfield, Simone, “The Social Indicators Final Project Report” (2017). PREP Reports & Publications. 409. https://scholars.unh.edu/prep/409 
Batiuk R, Breitburg DL, Diaz RJ, Cronin TM, Secor DH, Thursby G. 2009. Derivation of habitat-specific dissolved oxygen criteria for Chesapeake Bay and its tidal tributaries. Journal of Experimental Marine Biology and Ecology 381 (2009) 5204 – 5215
Batiuk R, Breitburg DL, Diaz RJ, Cronin TM, Secor DH, Thursby G. 2009. Derivation of habitat-specific dissolved oxygen criteria for Chesapeake Bay and its tidal tributaries. Journal of Experimental Marine Biology and Ecology 381 (2009) 5204 – 5215
Bierman, VJ, Diaz RJ, Kenworthy WJ, Reckhow, KH. 2014. Joint Report of Peer Review Panel for Numeric Nutrient Criteria for Great Bay Estuary. Pg 56. http://scholars.unh.edu/rtr/1/
Brabec, E, Schulte S, Richards PL. 2002. Impervious surfaces and water quality: A review of current literature and its implications for watershed planning. Journal of Planning Literature. 16(4). Pp.499-514
Bricker SB, Ferreira JG, and Simas T. 2003. An integrated methodology for assessment of estuarine trophic status. Ecological Modelling 169 (2003): 39 – 60.
Burdick, D., C. Peter, B. Fischella, M. Tyrrell, J. Allen, J. Mora, K. Raposa, J. Goldstein, C. Feurt, L. Crane. 2020. Synthesizing NERR Sentinel Site Data to Improve Coastal Wetland Management Across New England Data Report.  NEERS Science Collaborative. 34pp.
Canadian Council of Ministers of the Environment (CCME). 2003. Canadian water quality guidelines for the protection of aquatic life: Inorganic mercury and methylmercury. In: Canadian environmental quality guidelines, 1999. Canadian Council of Ministers of the Environment, Winnipeg. Publication No. 1299; ISBN 1-896997-34-1
Capone, M., R. Grizzle, A.C. Mathieson, and J. Odell (2008) Intertidal oysters in northern New England. Northeastern Naturalist 15, 209-215. 
Carballal MJ, Barber BJ, Iglesias D Villalba A. 2015. neoplastic diseases of marine bivalves. Journal of Invertebrate Pathology. 131 (2015) 83-106. 
EPA Office of Wastewater Management 2015 for examples https://www.epa.gov/sites/default/files/2015-12/documents/sw_utility_-_combined_slides_-_aug_13_2015.pdf
EPA resource 2009 https://www3.epa.gov/region1/npdes/stormwater/assets/pdfs/FundingStormwater.pdf 
Geoghegan, P., J. O’Brien, C.W. Walker, M. Heagy, and S. A. Böttger. 2021. Long-term trends in the occurrence of disseminated neoplasia in a population of Mya arenaria (Softshell Clam) from a New Hampshire estuary. Northeastern Naturalist 28(2):137-148.  
Glenn, M., Mathieson, A., Grizzle, R., & Burdick, D. (2020). Seaweed communities in four subtidal habitats within the Great Bay estuary, New Hampshire: Oyster farm gear, oyster reef, eelgrass bed, and mudflat. Journal of Experimental Marine Biology and Ecology, 524, 151307.
Glenn, M.E. (2016) “A Comparison of Macrofaunal and Algal Communities in Oyster Aquaculture Farm Gear, an Eelgrass Bed, Oyster Reef, and a Mudflat in Great Bay, New Hampshire” MS Theses. https://scholars.unh.edu/thesis/876.
Grizzle, R. and K. Ward (2020) “Assessing the success of NRCS-funded oyster reef restoration projects in New Hampshire from 2010–2018” Final Report. Dover, NH: Natural Resources Conservation Service. US Department of Agriculture.
Grizzle, R., Ward, K., Konisky, R., Greene, J., Abeels, H., & Atwood, R. (2021). Oyster Reef Restoration in New Hampshire, USA: Lessons Learned During Two Decades of Practice. Ecological Restoration, 39(4), 260-273.
Grizzle, R., Ward, K., Konisky, R., Greene, J., Abeels, H., & Atwood, R. (2021). Oyster Reef Restoration in New Hampshire, USA: Lessons Learned During Two Decades of Practice. Ecological Restoration, 39(4), 260-273.
Hartwick M, A Berenson, CA Whistler, EN Naumova, SH Jones. 2021.The Seasonal Microbial Ecology of Plankton and Plankton-Associated Vibrio parahaemolyticus in the Northeast US. Appl. Environ. Microbiol. 87:e02973-20. https://doi.org/10 .1128/AEM.02973-20.
Hayhoe K, Wake CP, Huntington TG, Luo L, Schwartz MD, Sheffield J, Wood E, Anderson B, Bradbury J, DeGaetano A, Troy TJ, Wolfe D. 2007. Past and future changes in climate and hydrological indicators in the US Northeast. Climate Dynamics. (2007) 28:381–407 https://doi.org/10.1007/s00382-006-0187-8
Jones SJ, Short FT, Webster M. 1992. Pollution. in “The Ecology of the Great Bay Estuary, New Hampshire and Maine: An Estuarine profile and bibliography.” ed., Short FT. NOAA Coastal Ocean Publication. http://scholars.unh.edu/prep/376
Jones, S H. 2000. A Technical Characterization of Estuarine and Coastal New Hampshire. A Report to the New Hampshire Estuaries Project. PREP Publications. Paper 294. http://scholars.unh.edu/prep/294 
Jones, S. 2000. A technical Characterization of estuarine and coastal New Hampshire. A report for the NH Estuaries Project (PREP). http://scholars.unh.edu/prep/294/
Jones, SH. 2021. Tracking Bacterial Contamination in the Lamprey River Watershed Final Report to the Lamprey Rivers Advisory Committee. November 2021. https://www.lampreyriver.org/application/files/6216/3856/5096/bacterial_tracking_FINAL_report.pdf.
Kemp, W.M., Batiuk, R., Bartleson, R., Bergstrom, P., Carter, V., Gallegos, C.L., Hunley, W., Karrh, L., Koch, E.W., Landwehr, J.M., Moore, K.A., Murray, L., Naylor, M., Rybicki, N.B., Stevenson, J.C., and Wilcox, D.J. 2004. Habitat Requirements for Submerged Aquatic Vegetation in Chesapeake Bay: Water Quality, Light Regime, and Physical-Chemical Factors. Estuaries, Vol. 27, No. 3 (Jun., 2004), pp. 363-377
Lemcke-Stampone, Mary D.; Wake, Cameron P.; and Burakowski, Elizabeth, “New Hampshire Climate Assessment 2021” (2022). The Sustainability Institute. 71. https://scholars.unh.edu/sustainability/71
Lemcke-Stampone, Mary D.; Wake, Cameron P.; and Burakowski, Elizabeth, “New Hampshire Climate Assessment 2021” (2022). The Sustainability Institute. 71. https://scholars.unh.edu/sustainability/71
Maine Department of Inland Fisheries and Wildlife. 2017. Beginning with Habitat Focus Areas. Augusta, Maine
Mallin MA, Williams KE, Esham EC, Lowe RP. 2000. Effect of Human Development on Bacteriological Water Quality in Coastal Watersheds. Ecological Applications, Vol. 10, No. 4 (Aug., 2000), pp. 1047-1056 Published by: Wiley on behalf of the Ecological Society. Stable URL: http://www.jstor.org/stable/2641016.
Metzger, M.J., A. Villalba, M.J. Carbrallal, D. Iglesias, J. Sherry, C. Reinisch, A.F. Muttray, S.A. Baldwin, and S.P. Goff. 2016. Widespread transmission of independent cancer lineages within multiple bivalve species. Nature 534:705–709.
Metzger, M.J., A.N. Paynter, M.E. Siddal, and S.P. Goff. 2018. Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla. Proceedings of the National Academy of Science 115:4277–4235.
Metzger, M.J., C. Reinisch, J. Sherry, and S.P. Goff. 2015. Horizontal transmission of clonal cancer cells causes leukemia in Soft-shell Clams. Cell 161(2):255–263. https://doi.org/10.1016/j.cell.2015.02.042.
Moore K. A., Shields E. C., Parrish D. B. (2014). Impacts of Varying Estuarine Temperature and Light Conditions on Zostera marina (Eelgrass) and Its Interactions With Ruppia maritima (Widgeongrass). Estuaries Coasts 37, 20–30. doi: 10.1007/s12237-013-9667-3
Morrell BK and CJ Gobler. 2020. Negative Effects of Diurnal Changes in Acidification and Hypoxia on Early-Life Stage Estuarine Fishes. Diversity. 2020, 12, 15 
New Hampshire Estuaries Project and Jones, Stephen H., “A Technical Characterization of Estuarine and Coastal New Hampshire” (2000). PREP Reports & Publications. 294. https://scholars.unh.edu/prep/294
New Hampshire Fish and Game Department and Grout, Douglas E., “Testing of Great Bay Oysters for Two Protozoan Pathogens” (2013). PREP Reports & Publications. 1.
https://scholars.unh.edu/prep/1
New Hampshire Fish and Game Department. 2020. Draft Comprehensive Plan for Resilient Salt Marsh in New Hampshire. Data available from: Great Bay National Estuarine Research Reserve, Greenland, NH.
New Hampshire Fish and Game Department. 2020. Wildlife Action Plan spatial data. Concord, New Hampshire.
NH Department of Business and Economic Affairs. 2021. Current estimates and trends in New Hampshire’s housing supply: Update 2021. https://www.nh.gov/osi/data-center/documents/housing-estimates-trends.pdf
NH Department of Environmental Services (NHDES). 2021. Status Report on the Occurrence of Per- And Polyfluoroalkyl Substance (PFAS) Contamination In New Hampshire. New Hampshire Department of Environmental Services, PO Box 95, Concord, NH 03302-0095. https://www4.des.state.nh.us/nh-pfas-investigation/wp-content/uploads/NH-PFASOccurrenceStatusReport12.27.2021-memo.pdf
NHDES. 2017. Status and trends of mercury in fish tissue in New Hampshire waterbodies, 1992 – 2016. Final Report, Concord, November 2017. [publication #R-WD-17-22]
NHDES. 2020 Stormwater Utilities: Funding Municipal Stormwater Programs https://www.des.nh.gov/sites/g/files/ehbemt341/files/documents/2020-01/stormwater-utilities.pdf
NHDES. Land Development. 2022. https://www.des.nh.gov/land/land-development#:~:text=The%20Alteration%20of%20Terrain%20(AoT,industrial%2C%20commercial%20and%20residential%20developments.
Normandeau 2021. Seabrook Station 2020 Environmental Monitoring in the Hampton-Seabrook Area. A Characterization of Environmental Conditions,  Chapter 7.0 Softshell Clam. Prepared for NextEra Energy Seabrook.
Odell, Jay; Eberhardt, Alyson L.; Burdick, David M.; and Ingraham, Pete, “Great Bay Estuary Restoration Compendium” (2006). PREP Reports & Publications. 150. https://scholars.unh.edu/prep/150
Payne, A.R., D.M. Burdick, G.E. Moore. 2019. Potential effects of sea level rise on salt marsh elevation dynamics in a New Hampshire estuary. Estuaries and Coasts 42:1405-1418. doi:10.1007/s12237-019-00589-z
PREP. 2010. Piscataqua Region Comprehensive Conservation and Management Plan, Piscataqua Region Estuaries Partnership: D.B.Truslow Associates, Mettee Planning Consultants, 2010, Durham, NH. scholars.unh.edu/prep/22
Runkel, RL, Crawford, CG, Cohn, TA. 2004. Load Estimator (LOADEST): A FORTRAN Program for Estimating Constituent Loads in Streams and Rivers: U.S. Geological Survey Techniques and Methods Book 4, Chapter A5, 69 p. https://doi.org/10.3133/tm4A5
Short, Frederick T.; Burdick, David M.; Wolf, Jaimie S.; and Jones, Galen E., “Eelgrass in Estuarine Research Reserves Along the East Coast, USA” (1993). PREP Reports & Publications. 393. https://scholars.unh.edu/prep/393 
Stasse A, Cheng MLH, Meyer K, Bumbera N, Van Volkom K, Laferriere AM, Dijkstra JA, Brown B. 2021. Temporal dynamics of Eastern Oyster Larval Abundance in Great Bay Estuary, New Hampshire. J. of Shellfish Research. 40(3): 471-478. 
Steckler P and Brickner-Wood D. 2019. Connect The Coast final report. Concord, NH.: The Nature Conservancy and the Great Bay Resource Protection Partnership.
Steckler P and Ormiston A. 2021. New Hampshire’s Coastal Watershed Conservation Plan, 2021 Update. The Nature Conservancy. Concord, NH
Steckler P, Glode J, and Flanagan S. 2016. Land Conservation Priorities for the Protection of Coastal Water Resources: A Supplement to The Land Conservation Plan for New Hampshire’s Coastal Watersheds. Prepared for the New Hampshire Department of Environmental Services Coastal Program. Technical Report, Concord, NH: The Nature Conservancy.
SWA model stormwater standards https://www.unh.edu/unhsc/sites/default/files/media/swa_stormwater-ord.pdf
Title 38: Waters and Navigation Chapter 3: Protection and Improvement of Waters Subchapter 1: Environmental Protection Article 2: Pollution Control   http://www.mainelegislature.org/legis/statutes/38/title38sec420-D.html
Trowbridge, P. 2009. Numeric nutrient criteria for the Great Bay Estuary. A report prepared for the NH Department of Environmental Services. https://www.des.nh.gov/sites/g/files/ehbemt341/files/documents/r-wd-09-12.pdf 
UNH Stormwater Center and Vanasse Hangen Brustlin, Inc. Minimizing Environmental Impacts Through Stormwater Ordinance and Site Plan Regulation (fact sheet). 2016. https://www.unh.edu/unhsc/sites/default/files/media/factsheet_-_p2_modelingrv_web.pdf
Urquhart EA, Jones SH, Yu JW, Schuster BM, Marcinkiewicz AL, Whistler CA, et al. (2016) Environmental Conditions Associated with Elevated Vibrio parahaemolyticus Concentrations in Great Bay Estuary, New Hampshire. PLoS ONE 11(5): e0155018. doi:10.1371/journal.pone.0155018  
US EPA. 2012. National Coastal Condition Report IV. https://www.epa.gov/national-aquatic-resource-surveys/national-coastal-condition-report-iv-2012
US EPA. 2012. National Coastal Condition Report IV. Office of Research and Development/Office of Water. EPA-842-R-10-003. https://www.epa.gov/sites/default/files/2014-10/documents/0_nccr_4_report_508_bookmarks.pdf 
Walker S, Smith T, Schumacher P, Czapiga J, Sowers D, Oman-Saltmarsh J, Dest P. 2010. The Land Conservation Plan for Maine’s Piscataqua Region Watersheds. Published by the Piscataqua Region Estuaries Partnership, Durham, NH. http://scholars.unh.edu/prep/32/
Wasson, K., Ganju, N., Defne, Z., Endris, C., Elsey-Quirk, T., Thorne, K.M., Freeman, C. M., Guntenspergen, G., Nowacki, D.J., and Raposa, K.B. 2019. Understanding tidal marsh trajectories: evaluation of multiple indicators of marsh persistence. Environmental Research Letters 14, 124073.
Weeks, JA, Guiney PD, Nikiforov AI. 2011. Assessment of the environmental fate and ecotoxicity of N, N-Diethyl-m-Toluamide (DEET). Integrated Environmental Assessment and Management. Volume 8, Number 1, p 120-134
Western Kentucky University Stormwater Utility Survey 2021 [https://digitalcommons.wku.edu/cgi/viewcontent.cgi?article=1003&context=seas_faculty_pubs]
Xu, F., S. Ilyas, J. A. Hall, S. H. Jones, V. S. Cooper & C. A. Whistler. 2015. Genetic characterization of clinical and environmental Vibrio parahaemolyticus from the Northeast USA reveals emerging resident and non-indigenous pathogen lineages. Front. Microbiol. 6: 272 
Zankel M, Copeland C, Ingraham P, Robinson J, Sinnott C, Sundquist D, Walker T, Alford J. 2006. The Land Conservation Plan for New Hampshire’s Coastal Watershed. PREP Publications. 174. http://scholars.unh.edu/prep/174/