You can understand a lot about the history, the difficulties and the successes and failures in the realm of water quality if you get two concepts: point source pollution and non-point source pollution.
Point source pollution runs from a pipe into a river or a lake. It's the easier of the two to identify and to fix (although such monumental battles as the Reserve Mining case in the 1970s have been fought over it.) To the extent that water quality has improved in Minnesota, it's largely the result of dealing in recent decades with point sources like sewage treatment plants and industrial operations by means of a national system of permits, regulatory limits and potential fines.
Non-point source pollution is harder to identify and to fix. It can include nitrates, phosphorus, bacteria and other materials that run off farmland, lakeshore property and developed urban land. Another water problem involves the presence of mercury, which typically gets into water from the air and whose source is similarly difficult to pinpoint. Efforts to deal with non-point source pollution tend to involve looking at networks of land and water use and trying to educate and change the behavior of many people and organizations.