They've been over-fished, the industries of the surrounding area polluted the living hell out of them up until the 1970's, they've been invade by Zebra mussels and the water levels are at record lows.
Fisheries adapted. Pollution has seen a massive decline. The zebra mussel...well that's nature, and as much as can be done about it has been done, but you can't really stop nature. As to water levels --
http://www.waterlevels.gc.ca/C&A/NetworkMeans2013.pdf
-- it's at a low ebb right now, but isn't at record lows at all. If you have memories of much higher levels, those were likely historic highs.
Plenty is being done for the Great Lakes. More can be done, but pointing back at the 70s doesn't demonstrate that things aren't being done today.