We examined patterns of fish community composition and the relation to environmental variation in a drowned river mouth system of Lake Michigan. Direct hydrological connections to the Muskegon River and Lake Michigan contribute to a unique ecosystem with large‐lake and riverine influences, thus making Muskegon Lake of particular interest for assessing fish community structure across spatiotemporal scales. Using overnight fyke‐net sets, we sampled the fish community at four littoral sites in Muskegon Lake during spring, summer, and fall of 2003–2009; we also measured a suite of physicochemical variables at each sampling location and event. Among the most abundant species captured were the yellow perch Perca flavescens, round goby Neogobius melanostomus, and bluntnose minnow Pimephales notatus. Results from nonmetric multidimensional scaling showed that fish assemblages varied strongly across seasons and across sites but that annual variation was weak. Canonical correspondence analysis by season showed that temperature was the most important variable in spring, whereas turbidity, dissolved oxygen, and depth were more influential in structuring fish communities during summer. Macrophyte cover played a significant role in explaining community composition in the fall. We observed patterns of seasonal temporal variation in species–environment relationships, similar to patterns observed in purely lacustrine systems. We also observed patterns of fine‐scale spatial variation, which are typically noted in purely riverine systems. As such, our results have implications for predicting and determining patterns in other drowned river mouth lakes and reservoirs that are heavily influenced by both riverine and large‐lake dynamics.