Strategic Plan for the Restoration of Diadromous Fishes to the Penobscot River Prepared By: Department of Marine Resources Department of Inland Fisheries and Wildlife For Presentation to the Atlantic Salmon Commission: Dick Ruhlin, Chair, Member-at-large George Lapointe, Commissioner of the Department of Marine Resources R. Dan Martin, Commissioner of the Department of Inland Fisheries and Wildlife March 2008 2 Table of Contents List of Acronyms ............................................................................................................................. 4 Executive Summary......................................................................................................................... 5 Introduction..................................................................................................................................... 6 Vision .............................................................................................................................................. 9 Description of the Basin.................................................................................................................. 9 Sub-Watersheds ........................................................................................................................... 9 River hydrology ......................................................................................................................... 10 Barriers ..................................................................................................................................... 10 Stream Water Quality Classification and Monitoring .............................................................. 12 Point Source Discharges ........................................................................................................... 13 Posted fish consumption advisories .......................................................................................... 13 Other environmental issues ....................................................................................................... 13 Fishes of the Penobscot River Basin............................................................................................. 14 Status of Stocks ............................................................................................................................. 14 Atlantic Salmon ......................................................................................................................... 14 American shad .......................................................................................................................... 16 Alewife ....................................................................................................................................... 18 Blueback herring ....................................................................................................................... 20 American eel ............................................................................................................................. 21 Rainbow Smelt .......................................................................................................................... 22 Shortnose sturgeon and Atlantic sturgeon ................................................................................ 23 Striped bass ............................................................................................................................... 24 Atlantic tomcod and sea lamprey .............................................................................................. 25 Resident Species ........................................................................................................................ 25 Foundation.................................................................................................................................... 25 Overall Goal of the Plan............................................................................................................... 28 Strategic Goals, Objectives and Strategies................................................................................... 28 Additional Elements Necessary for Recovery............................................................................... 37 Research Needs ......................................................................................................................... 37 Funding ..................................................................................................................................... 37 Hatchery Capacity .................................................................................................................... 40 Outreach and Education ........................................................................................................... 40 Literature Cited............................................................................................................................. 41 Table 1. Major sub watersheds (HUC 8) in the Penobscot River, Maine ................................... 47 Table 2. Water discharge data...................................................................................................... 47 Table 3. Upstream and Downstream Fish Passage Facilities, Penobscot River Drainage......... 48 Table 4. Fishes of the Penobscot River basin............................................................................... 49 Table 5. Production estimates for American shad........................................................................ 53 Table 6. Production estimates for alewife. ................................................................................... 54 Table 7. MDIFW cold and warm water management areas and waters by drainage area with management .................................................................................................................................. 56 Table 8. Species to be passed at hydropower projects in the Penobscot basin............................ 62 Strategic Plan for the Restoration of Diadromous Fishes to the Penobscot River March 2008 3 Figure 1. Simplified spatial and temporal overlap of diadromous fishes in the Penobscot River ecosystem, where arrows represent peak activity periods............................................................ 63 Figure 2 . Penobscot River subwatersheds.................................................................................. 64 Figure 3. Location of barriers in the Penobscot River basin. ..................................................... 65 Figure 4. Penobscot Basin water quality...................................................................................... 66 Figure 5. Location and type of point source discharges in the Penobscot basin......................... 67 Figure 6. Location of fish health advisories. ................................................................................ 68 Figure 7. Number of Atlantic salmon returning to the Penobscot River and other rivers in New England from 1970 to 2006. ......................................................................................................... 69 Figure 8. Number and origin (hatchery or wild/naturally reared) Atlantic salmon returning to the Penobscot River from 1970 to 2006........................................................................................ 69 Figure 9. Return rate of 1SW and 2SW adults by cohort of hatchery-reared Atlantic salmon smolts released into the Penobscot River. .................................................................................... 70 Figure 10. Number of juvenile Atlantic salmon stocked in the Penobscot River from 1970 to 2006............................................................................................................................................... 70 Figure 11. Historical habitat of American shad........................................................................... 71 Figure 12. Accessibility of American shad spawning habitat before (top) and after (bottom) the Penobscot River Restoration Project............................................................................................ 72 Figure 13. Historical migration routes and lake/pond spawning habitat of alewives in red; habitat in purple may not have been inaccessible. ....................................................................... 73 Figure 14. Accessibility of alewife spawning habitat before (top) and after (bottom) the Penobscot River Restoration Project............................................................................................ 74 Figure 15. Number of American eel captured per km electrofishing .......................................... 75 Appendix A. A Historical Context for the Native and Commercial Fisheries of the Penobscot River.............................................................................................................................................. 76 Appendix B. Agency Missions and Goals ..................................................................................... 87 Appendix C. Standards for classification of fresh surface waters ............................................... 88 Appendix D. Methodology for total production estimates of American shad and alewife. ......... 92 Appendix E: Conceptual Restoration Monitoring Plan for Fisheries Resources Affected by the Penobscot River Restoration Project............................................................................................ 94 Strategic