Fish assemblages from three of the New York Finger Lakes were examined for structure within and between lakes and over time. Species-area relationships indicated that local fish assemblages are the result of recent, lake-specific events that altered the regional species pool. Fish assemblages varied among seasons and those occupying eutrophic waters had different characteristics from those in oligotrophic waters. Bluntnose minnows (Pimephales notatus) were a persistent and important component of most assemblages, but abundance of bluegill (Lepomis macrochirus) was the most distinguishing feature. Species associations indicated that interactions among the fishes had little influence on assemblage structure. Correlations between community structure and abiotic factors were identified. Ten abiotic variables were strongly associated with the species assemblages, but could not fully explain differences between assemblages. Results indicate that the abundance and diversity of water column feeders was related to productivity of lake habitat. In general, fish populations were smaller in oligotrophic waters and water column feeders were poorly represented in those assemblages. Productivity at various trophic levels was implicated as a major factor determining lake fish assemblage structure.