Pugnose Shiner lives in near-shore areas of Lake Ontario bays, the Saint Lawrence River and Cayuga Lake where submerged aquatic vegetation dominates and has been reported in three of 18 watersheds. It is extirpated from Cayuga Lake, Oswego watershed. In Lake Ontario it has declined in two of the three historic populations. There are more populations now than were reported historically in bays in the Saint Lawrence River. It is sensitive to change in these special habitats dominated by aquatic vegetation and is classified as Endangered.