Most of the pollution in the waterways comes from agriculture and town/city run-off. Old school paper mills and other factory type operations didnt help, but the long term accumulated water pollution is from bad agricultural practices and towns/cities.
Every town in Alabama is on some kind of creek or directly on a river. Over time, our daily living makes its way into the watershed. Decades of herbicides, pesticides, and high chemical fertilizers, also make their way into the watersheds.