Biological valuation of Atlantic salmon habitat within the Gulf of Maine Distinct Population Segment Biological assessment of specific areas currently occupied by the species; and determination of whether critical habitat in specific areas outside the currently occupied range is deemed essential to the conservation of the species NOAA’s National Marine Fisheries Service Northeast Regional Office 1 Blackburn Drive Gloucester, MA. 01930 2009 Foreword: Atlantic salmon life history........................................................................................................... 3 Chapter 1: Methods and Procedures for Biological Valuation of Atlantic Salmon Habitat in the Gulf of Maine Distinct Population Segment (GOM DPS).......................................................................................... 6 1.1 Introduction .............................................................................................................................................. 6 1.2 Identifying the Geographical Area Occupied by the Species and Specific Areas within the Geographical Area ................................................................................................................................................................ 7 1.3 Specific areas outside the geographical area occupied by the species essential to the conservation of the species .......................................................................................................................................................... 11 1.4 Identify those “Physical and Biological Features” in freshwater and estuary specific areas that are essential to the conservation of the species .................................................................................................. 16 1.4.1 Conservation defined....................................................................................................................... 17 1.4.2 Physical and biological features needed by Atlantic salmon........................................................... 17 (A). Physical and Biological Features of the Spawning and Rearing PCE......................................... 18 (B). Physical and Biological Features of the Migration PCE ............................................................. 22 (C). Physical and biological features of marine sites and “Specific Areas” within the geographic range occupied by the species .............................................................................................................. 25 1.5 Identify special management considerations and protections................................................................. 25 1.5.1 Specific activities that may effect physical and biological features ................................................ 27 Agriculture............................................................................................................................................ 27 Forestry ................................................................................................................................................ 28 Changing land-use and development.................................................................................................... 29 Hatcheries and stocking ....................................................................................................................... 31 Roads and road crossings..................................................................................................................... 31 Mining .................................................................................................................................................. 32 Dams..................................................................................................................................................... 33 Dredging............................................................................................................................................... 33 Aquaculture .......................................................................................................................................... 34 1.6 Procedure used to determine biological value of habitat within specific areas ...................................... 37 1.6.1 Methods and procedures used to determine the biological value of HUC 10 watersheds ............... 37 Habitat units......................................................................................................................................... 37 Habitat quantity.................................................................................................................................... 37 Habitat quality...................................................................................................................................... 38 Final habitat value ............................................................................................................................... 40 Final Migration Value.......................................................................................................................... 40 Final Biological Value.......................................................................................................................... 40 Chapter 2: Downeast Coastal SHRU Biological Report.............................................................................. 41 2.1 Landscape and hydrologic features that shape the physical and Biological features within the Downeast Coastal SHRU .............................................................................................................................................. 41 2.1.1 Geography ....................................................................................................................................... 41 2.1.2 Geology and climate........................................................................................................................ 41 2.1.3 Hydrology........................................................................................................................................ 42 2.1.4 Natural barriers................................................................................................................................43 2.2 Human influence on Downeast Coastal SHRUU ...................................................................................... 44 2.2.1 Current population structure and land-use....................................................................................... 44 2.2.2 Dams and barriers to fish passage ................................................................................................... 44 2.2.3 Water Quality .................................................................................................................................. 45 2.2.4 Fisheries and fish introductions in the Downeast Coastal SHRU.................................................... 47 2.3 Atlantic salmon habitat........................................................................................................................... 49 Chapter 3: Penobscot Bay SHRU Biological Report................................................................................... 54 3.1 Landscape and hydrologic features that shape the physical and biological features within the Penobscot SHRU ........................................................................................................................................................... 54 3.1.1 Geography ....................................................................................................................................... 54 3.1.2 Geology and climate........................................................................................................................ 54 3.1.3 Hydrology........................................................................................................................................ 54 3.1.4 Natural barriers................................................................................................................................56 3.2 Human Influence on the Penobscot SHRU.............................................................................................U 57 1 3.2.1 Current population structure and land use ....................................................................................... 57 3.2.2 Dams and diversions........................................................................................................................ 57 Penobscot River restoration effort through dam removal .................................................................... 58 3.2.3 Fisheries and fish introductions in the Penobscot SHRU ................................................................ 60 3.3 Atlantic salmon habitat........................................................................................................................... 63 Chapter 4: Merrymeeting Bay SHRU Biological Report ............................................................................ 70 4.1 Landscape and hydrological features that shape the physical and biological features within the Merrymeeting Bay SHRU ............................................................................................................................ 70 4.1.1 Geography ....................................................................................................................................... 70 4.1.2 Geology and climate.......................................................................................................................