I've been reading Environmental Law, William H. Rodgers, Jr., from the UW School of Law. There seems to be debate over whether dams should be covered as point or non-point source provisions of the Clean Water Act. The pollution problems associated with dams include: low dissolved oxygen, dissolved minerals and nutrients, water temperature rise, sediment release, and superaturation of nitrogen.

I checked Marty's steelheader.net site and found a link to a recent article (EPA rekindles old debate...) at columbia.com where this debate has resurfaced.