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Seafloor communities in a restricted fishing area in NOAA’s Stellwagen Bank National Marine Sanctuary are showing indications of recovery from chronic fishing gear impacts but are not fully stable. The National Marine Sanctuary Act (NMSA) requires that marine sanctuaries are managed to allow multiple uses (e.g., fishing), assuming that those activities are compatible with the primary goal, which is resource protection. However, there are no clear metrics and reference points to trigger management actions and information to guide decision-making is often fragmented and incomplete. The need to balance human uses of the marine environment with the conservation of biological diversity requires knowledge of how particular activities affect diverse populations and communities within particular habitats.