Coastal embayments have been and will continue to be constructed along the northwest shoreline of Lake Ontario to restore and create warmwater fish habitat. However, very little is known about the biological connections among embayments. Using otolith microchemistry on pumpkinseed, largemouth bass and yellow perch collected from three constructed embayments in 2006–2009, we confirm that these three species of fish each exist in a metapopulation. We find that juvenile pumpkinseed, largemouth bass and yellow perch occupy embayments different from their natal habitat after their first winter, and for at least pumpkinseed, continue to move among embayments after their second winter. We hypothesize that these fishes move among embayments after haphazardly dispersing from their overwintering habitat to the littoral zone each spring. Habitat restoration and remediation efforts in coastal Great Lakes habitats should take a system-based management approach that considers the spatial proximity of embayments, and attempts to create or preserve connected networks.