The lakes, ponds and streams in the park are homes for the frogs, turtles, perch, bass, and pike, as well as, the wealth of mayflies, dragonflies, black flies, stone flies, and caddis flies. There are many waterfowl species that use these water resources for nesting or resting during migration and even during the winter in the unfrozen portions of the streams. Shorebirds are constantly combing the waters edge for a tasty morsel. Scientific studies of the lakes and streams indicate that they are currently clean, healthy aquatic systems, but that they are also at risk from pollution, invasion by exotic species, and overuse.
There are 26 lakes and ponds in the Lakeshore as well as a variety of wetlands and bogs. They provide excellent recreation opportunities for the park visitor for canoeing, fishing, and wildlife viewing. The park restricts the use on most of the small lakes to non-motorized boats in order to preserve the quality of the resource and the visitor experience. Many of the lakes in the wilderness-designated portions of the Lakeshore offer a quiet, and peaceful chance to enjoy nature at its best.