If you've been around the Great Lakes recently, you might notice they don't ascribe to the pristine standards you were expecting from what you remember (or what you've heard from people who grew up around the Great Lakes). Although most individuals will focus on the effects of point-source pollution, climate change is having an equally serious impact. 

As to the issue of water levels, researchers on both sides of the global warming fence have attributed it to factors that support their respective viewpoints: the environmentalists cite studies that say it's all man's doing, while the global warming naysayers find experts who attribute everything to natural causes. Although no one's entirely sure whose verdict is the ultimate truth, scientists have agreed on one simple thing: humans are destroying the Great Lakes through climate change. The destruction isn't limited to the amount of water itself but extends, among other things, to the ecosystems and the habitats of those living within the lake and outside of it.

The Great Lakes, as one of the few freshwater sources left in the world, has a very specific biological and chemical makeup, which is highly sensitive to anthropogenic influences. The aquatic species living in the Great Lakes have adapted, over millions of years, to the temperatures, oxygen levels and seasonal variations that occur in their habitat. It would take another million or more years for them to adapt to changes in that, if they are even capable of such adaptation.

Even if species aren't living inside the Lakes, their habitat and ability to survive is being drastically affected. Just imagine what would happen if ducks stopped migrating to certain areas around the Great Lakes because the climate wasn't just right. Surely, they would find somewhere else to go-at least for the time being, but what about after that. What about when those areas became too warm? This phenomenon is occurring right now and its damage is changing more than just the ducks' migration routes. It is, after all, called the food chain. What happens to a chain with a missing link?

It's not a chain anymore.

Likewise, the Great Lakes without their native habitats, resources, vegetation, wildlife and climate aren't so great anymore.

Sources:

http://www.climatehotmap.org/impacts/greatlakes.html
http://www.sciencedaily.com/releases/2009/01/090113101122.htm
http://www.detnews.com/article/20090502/METRO/905020351/1409/METRO/Study--Ice-jam-caused-Great-Lake-water-levels-to-drop
http://www.mlive.com/business/ann-arbor/index.ssf/2009/07/guest_opinion_great_lakes_wate.html