We surveyed little-known ray-finned fish assemblages from Maryland's coastal bays in order to establish species-habitat relationships for common species. From 1996–1999, 25 sites were sampled monthly with otter trawls in the coastal bays of Maryland. Anchoa mitchilli (bay anchovy) constituted nearly 50% of the catch for each year, and species composition was largely similar across years, with some differences likely related to variation in recruitment. For example, Clupea harengus (Atlantic herring) was particularly abundant during 1996 and 1999 following their spawning season. We used canonical correspondence analysis to determine how assemblages were related to temperature, dissolved oxygen (DO), salinity, and land-use variables during summer (June–September) and throughout the rest of the year. A gradient correlated with temperature and DO significantly structured assemblages throughout most of the year; during summer, the proportion of wetland habitat was important. We demonstrate that environmental gradients important for structuring fish assemblages differ between summer and non-summer months and there is a general shift in habitat use during summer from the lower estuary to other areas of the coastal bays. Our data also provide support for earlier observations that temperature was the major factor influencing changes in fish assemblage structure in the coastal bays. Our results point to better characterization of fish habitats in order to effectively manage coastal ecosystems of Maryland.