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Along the Gulf ofAlaska, rapid glacier retreat has driven changes in transport of freshwater, sediments, and nutrients to estuary habitats. Over the coming decades, deglaciation will lead to a temporary increase, followed by a long-term decline of glacial influence on estuaries. Therefore, quantifying the current variability in estuarine fish community structure in regions predicted to be most affected by glacier loss is necessary to anticipate future impacts. We analyzed fish community data collected monthly (April through September) over 7 years (2013–2019) from glacially influenced estuaries along the southeastern Gulf of Alaska. River delta sites within estuaries were sampled along a natural gradient of glacial to non-glacial watersheds to characterize variation in fish communities exposed to varying degrees of glacial influence. Differences in seasonal patterns of taxa richness and abundance between the most and least glacially influenced sites suggest that hydrological drivers influence the structure of delta fish communities. The most glacially influenced sites had lower richness but higher abundance overall compared to those with least glacial influence; however, differences among sites were small compared to differences across months. Two dominant species—Pacific staghorn sculpin and starry flounder—contributed most to spatial and temporal variation in community composition; however, given only small interannual differences in richness and abundance over the period of the study, we conclude that year-to-year variation at these sites is relatively low at present. Our study provides an important benchmark against which to compare shifts in fish communities as watersheds and downstream estuaries continue to transform in the coming decades.