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The Federal Energy Regulatory Commission (FERC) regulates most hydropower dams in the United States and grants operational licenses that include conditions for the conservation of sea‐run fish. FERC is the primary authority in relicensing, but the process invites input from other federal and state resource agencies. As a result, relicensing decisions often reflect trade‐offs among competing authorities, values and objectives. FERC relicensing decisions in the Kennebec and Penobscot Rivers in Maine were assessed to characterise agency engagement and identify factors that influence fish passage decisions. Qualitative and quantitative analysis of FERC project documents from 1984 to 2019 showed that conservation measures are focused almost exclusively on Atlantic salmon, Salmo salar L., and American eel, Anguilla rostrate Leseur. Incorporation of fish passage mitigation requirements has increased coincident with increased agency engagement and the use of regulatory authority. Strong fish passage prescriptions are found at coastal projects (where sea‐run fish exist) likely resulting from both state and federal agency input. Despite wide interest in basin‐scale and interagency fish passage planning, implementation of collaborative processes has been slow, with most dams being considered and licensed individually. As a result, there are opportunities to spatially integrate the FERC process in the future and support effective stakeholder engagement. [ABSTRACT FROM AUTHOR]