"Large corn and soy farms are mostly to blame, scientists and activists say, because they rely heavily on large quantities of phosphorous- and nitrogen-rich fertilizer that leach into the lakes, where they feed toxic blooms of cladophora and other nasty algae species. Manure from factory farms only adds to the nutrient load. [...] Farmers retort by pointing out that many households are also wasteful when it comes to the use of lawn fertilizers, which enter the lakes through storm-water drains."Michigan Tech has a longer piece explaining some more of the science. Ugh.
Science Last September, Grist reported on how a toxic green slime regularly covers the surfaces of the great lakes and it's man-made: