Earlier quoted context omitted.
With the size of the Great Lakes, it wouldn't be that surprising that some bays or inlets would be clean while others were disgusting. I don't know about Lake Michigan, but I wouldn't really have advocated swimming in the parts of Lake Ontario I was around in the '80s.
I was living in Toronto in the 1990's and I wouldn't swim in Lake Ontario if you paid me. And anyway this is a seasonal effect brought on by a larger than usual ice content this past winter. If I read the article correctly this won't last long and run off from surrounding farms and industry will have the lake algae ridden and opaque before too long...
I think a city's relationship with its waterfront has to do with what was built on land next to the water. In Toronto the lakefront was industrial until recently. In Chicago the industry was clustered along the river and the lakefront has consisted of parks and beaches for a century.