Rapids habitats are critical spawning and nursery grounds for multiple Laurentian Great Lakes fishes of ecological importance such as lake sturgeon, walleye, and salmonids. However, river modifications have destroyed important rapids habitat in connecting channels by modifying flow profiles and removing large quantities of cobble and gravel that are preferred spawning substrates of several fish species. The conversion of rapids habitat to slow moving waters has altered fish assemblages and decreased the spawning success of lithophilic species. The St. Marys River is a Great Lakes connecting channel in which the majority of rapids habitat has been lost. However, rapids habitat was restored at the Little Rapids in 2016 to recover important spawning habitat in this river. During the restoration, flow and substrate were recovered to rapids habitat. We sampled the fish community (pre- and post-restoration), focusing on age-0 fishes in order to characterize the response of the fish assemblage to the restoration, particularly for species of importance (e.g. lake whitefish, walleye, Atlantic salmon). Following restoration, we observed a 40% increase in age-0 fish catch per unit effort, increased presence of rare species, and a shift in assemblage structure of age-0 fishes (higher relative abundance of Salmonidae, Cottidae, and Gasterosteidae). We also observed a “transition” period in 2017, in which the assemblage was markedly different from the pre- and post-restoration assemblages and was dominated by Catostomidae. Responses from target species were mixed, with increased Atlantic salmon abundance, first documented presence of walleye and no presence of lake sturgeon or Coregoninae.