Finfish abundance indices, produced from seasonal trawl survey data collected in Long Island Sound, were examined for changes in community composition related to the dynamics of water temperature from 1984 to 2008. In general, seasonal mean catch of species identified a priori as cold adapted significantly decreased while warm-adapted and subtropical species significantly increased over the time series. Bottom water temperature also significantly increased. As a group, annual abundance of cold-adapted species exhibited significant negative correlation with mean bottom water temperatures while warm-adapted species, but not subtropical species, exhibited significant positive correlation. Multivariate analyses identified a shift in community structure producing two primary year-groupings. Spring groupings were clearly delineated as 1984–1998 (cold period) and 1999–2008 (warm period). Autumn groupings were temporally discontinuous in the 1990s with group membership shifting between cold and warm periods, although the distal ends of the time series were clearly divided. These patterns aligned with deviations from the 1984 to 2008 mean bottom water temperature, indicating that this estuary is experiencing a relatively rapid shift consistent with a response to climate warming. The more distinct delineation of community structure in spring suggests that the lack of advantageous spring conditions was a more important factor in the decline of cold-adapted species than increasingly stressful conditions in autumn.