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In 2012, Hurricane Sandy created a new tidal inlet at Fire Island National Seashore (FIIS) in New York, USA, consequently altering environmental conditions within Great South Bay. This event presented a unique opportunity to establish new ecological baselines, assess resulting ecological change, and explore management implications. This study focuses on benthic mapping within the bayside of FIIS using acoustic, grab sample, and imagery data. Biotope (habitat) maps were developed describing relationships between macrofaunal communities and their environment. Additionally, biotopes were prioritized by “ecological value” based on user-defined criteria (presence of seagrass and potential for higher trophic level interactions) to guide management. While there are limited pre-Sandy data for comparison, findings from this study suggest the inlet has been a positive ecological influence on the nearby area. Dense concentrations of mature blue mussels (Mytilus edulis) documented near the inlet are considered ecologically beneficial and represent a post-Sandy distinction in ecosystem structure; M. edulis was last common when the inlet was previously open (early 1800s). The inlet is also likely responsible for seagrass expansion near the inlet but decline in other areas. This study advances the utility of the Coastal and Marine Ecological Classification Standard (CMECS) by including CMECS-defined data in analyses and expanding the definition of “dominance.” CMECS played a key role in developing map units, interpreting biotopes, and establishing statistically significant and ecologically meaningful biotic–abiotic relationships. This study also highlights the value and management applications of benthic mapping specific to FIIS and more broadly and advocates for similar studies elsewhere.