A recent study investigated the cumulative effects of human activities on the health of the Great Lakes, and concluded that Lakes Erie, Ontario, and Michigan face the greatest threats, while Like Superior is the least threatened. The most stressed areas are along coastlines, especially near major metropolitan areas, which is not surprising. Threats include invasive species (especially zebra mussels and lampreys), climate change (affecting lake temperature and water levels), phosphorous from erosion of agricultural soils, and contaminants from urban areas. Stressed areas almost always have multiple stressors, complicating restoration efforts. The authors of the study note that restoration efforts in the Great Lakes are almost exclusively focused on high-stress sites, but almost never have information about the full range of stressors.

I recently presented a webinar on the effects of road salt on water resources, and one of the figures I showed was from a paper that showed historic chloride concentrations in the Great Lakes (Chapra et al. 2009. J. Great Lakes Research 35(2):272-284):

In the Midwest, all chloride contamination is due to human activities. You can see how Lakes Erie and Ontario, and, to a lesser extent, Lake Michigan, show contamination since the late 1800s. Notice that around 1970 chloride levels began to drop in Lakes Erie and Ontario, presumably due to the passage of the Clean Water Act that resulted in the clean-up of the worst pollution sources. But starting in the 1980s, chloride levels have started to go back up, and this is almost certainly due to increased road salt runoff. The graph below shows road salt sales in the U.S.: 

One of the reasons that there is more variability in the water quality in Lakes Erie and Ontario compared to Lake Michigan is their much shorter residence times, less than 3 years for Erie and about 6 years for Ontario. Water enters those lakes on the western end and flows in a relatively straightforward manner to the eastern end where it exits. Water stays in Lake Michigan for a much longer period, almost 100 years, traveling in a counterclockwise direction around the lake. So it’s easier to pollute Lake Erie than Lake Michigan, but more difficult to clean up Lake Michigan.