The NPDES program primarily focuses on reducing pollutants in industrial process wastewater and discharges from municipal sewage treatment plants. There are also effluent limits in storm water permits issued under NPDES. The program does not exempt sources based on the levels of pollutants in receiving waters. Discharges that do not require NPDES permits are listed in 40 CFR 122.3. Applicability of storm water permit requirements can be found in 122.26.
EPA also issues effluent guidelines for categories of dischargers under Title III of the Clean Water Act. The standards are technology-based (i.e. they are based on the performance of treatment and control technologies). Here again, the limits are not based on risk or impacts upon receiving waters. Effluent guidelines and standards for sources begin at 40 CFR Part 401.