Recent investigations in the Detroit River have revealed renewed spawning activity by several important fishes, but little is known about their early life history requirements. We surveyed two main channel and two backwater areas in the lower Detroit River weekly from May to July 2007 to assess habitat use by larval fishes. Backwater areas included a soft-sediment embayment (FI) and a hard-sediment area (HIW). Main channel sites were located adjacent to each backwater area. Water temperature, velocity and clarity measurements and zooplankton samples were collected weekly. A macrophyte assessment was conducted in July. Growth and diet of larval yellow perch (Perca flavescens), bluegill (Lepomis macrochirus) and round goby (Neogobius melanostomus) were used to assess habitat quality. Macrophyte diversity and percent cover were higher and velocity lower at FI than HIW. Although larval fish diversity was highest in the main channel, yellow perch and bluegill larvae only grew beyond the yolk stage at FI, where they preferentially selected copepods, while Daphnia were selected in the main channel. Round goby ate harpacticoid copepods and Daphnia and grew at similar rates in HIW and the main channel. These data indicate that FI was a valuable nursery area for yellow perch and bluegill, whereas HIW was better suited to round goby. We only assessed two backwater areas, thus a complete census of wetland areas in the Detroit River is needed to identify valuable habitats. Restoration of shallow backwater areas is essential for rehabilitating fish populations and should be a priority in the Detroit River.