Humans have basically caused the problem in the first place. Bad pipes leaked lead into the water and it was not treated correctly. Maybe Michigan's watershed was clean at first and when lead started leaking in it couldn't get absorbed by the land (do to buildings and land development) and it stayed in the water.
The main reason that there was lead and other dangerous things in the water was insufficient water treatment. This was likely caused by trying to save money for Michigan. They didn't apply corrosion inhibitor to the water that keeps it safe.
Michigan wanted to save a lot of money so they switched there water supply from lake Huron to the very dirty Flint river. Other factors also amplified the issue such as corroded pipes that let in more lead and other things to make dirty drinking water.