Despite its immensity, the aquatic ecosystem of Lake Huron area is also under increasing pressure from human activities. Ninety-nine percent of the water in the Lake Huron – Georgian Bay basin is of glacial origin, with only 1% being replenished by rainfall. It is thus effectively a finite resource. It has long been known that dredging of the St. Clair River, the outlet of the waters of lakes Huron and Michigan has resulted in a permanent lowering of the level of the lake (Derecki 1985). The impacts of accellerated global climate change and municipal pipelines on the natural fluctuations of the lake are less well known. In any case, human activities are at least partly responsible for the current low water levels. Unless the causes are mitigated or reversed, low lake levels may significantly affect the quality of wetland and shoreline habitats of Georgian Bay, not to mention recreational and commercial activities along the coast. Natural fluctuations of several of the interior riverine aquatic ecosystems have also been compromised by hydroelectric and flood-control dams.

Problems with the aquatic ecosystem are not new, as overfishing led to the collapse of the regional commercial fishery in the early 1900’s. However, in comparison with the other Great Lakes, Lake Huron’s aquatic community health and biodiversity are relatively good. The fish communities of Lake Huron are recovering after decades of over-harvest and competing populations of non-indigenous species.