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Abstract Rapid changes in sea ice extent and changes in freshwater inputs from land are rapidly changing the nature of Arctic estuarine ecosystems. In the Beaufort Sea, these nearshore habitats are known for their high productivity and mix of marine resident and diadromous fishes that have great subsistence value for Indigenous communities. There is, however, a lack of information on the spatial variation among Arctic nearshore fish communities as related to environmental drivers. In summers of 2017–2019, we sampled fishes in four estuarine ecosystems to assess community composition and relate fish abundance to temperature, salinity, and wind conditions. We found fish communities were heterogeneous over larger spatial extents with rivers forming fresh estuarine plumes that supported diadromous species (e.g., broad whitefishCoregonus nasus), while lagoons with reduced freshwater input and higher salinities were associated with marine species (e.g., saffron codEleginus gracilis). West–East directional winds accounted for up to 66% of the community variation, indicating importance of the wind-driven balance between fresh and marine water masses. Salinity and temperature accounted for up to 54% and 37% of the variation among lagoon communities, respectively. Recent sea ice declines provide more opportunity for wind to influence oceanographic conditions and biological communities. Current subsistence practices, future commercial fishing opportunities, and on-going oil and gas activities benefit from a better understanding of current fish community distributions. This work provides important data on fish spatial distributions and community composition, providing a basis for fish community response to changing climatic conditions and anthropogenic use.