The seasonal variation of the inshore fish assemblage of Anegada Bay, North Patagonia, Argentina is described here. Three areas were seasonally sampled from 2007 to 2009 by means of a gang of bottom gill-nets. We found 21 coastal fish species, but species richness and fish number and weight changed throughout the year. The six species classified as dominant have national and regional value for artisanal and recreational fishing and were responsible for the seasonal variation in the fish assemblage. Both cluster and non-metric multidimensional scaling analyses based on fish number and fish weight indicated two major sample groups encompassing spring and summer (the warmer seasons) and autumn and winter (the colder seasons). The fish assemblage had higher species richness, dominance and abundance during the warmer seasons than during the colder seasons in the same years and at the same sites. Water temperature was the main environmental factor structuring the fish assemblage in Anegada Bay. We suggest that partial breeding migration toward the bay during warmer months could explain the seasonal pattern observed. Nevertheless, variation in temperature conditions agreed well with the pattern of seasonal changes, leading to an interaction between abiotic and biotic influences in determining the variability in this seasonal fish assemblage. We conclude that an understanding of species temporal and spatial patterns in areas of high ecological and economic value, as exemplified by Anegada Bay, are essential for the implementation of a management approach oriented toward ecosystem sustainability.