The city of Aberdeen is required to obtain coverage under the Western Washington Phase II municipal stormwater permit through the National Pollutant Discharge Elimination System and State waste discharge general permit for discharges from small municipal separate storm sewers in Western Washington. This permit is in compliance with the provisions of the State of Washington Water Pollution Control Law, Chapter 90.48 RCW, and the Federal Water Pollution Control Act (the Clean Water Act), Title 33 U.S.C., §  1251 et seq.

Under the Federal Clean Water Act, the National Pollutant Discharge Elimination System (NPDES) permit program controls water pollution by regulating point sources that discharge pollutants into waters of the United States. The NPDES stormwater program requires the implementation of stormwater programs. Phase II of the NPDES rules extends coverage to operators of regulated small municipal separate storm sewer systems (MS4s) serving less than one hundred thousand (100,000). The Washington State Department of Ecology develops and administers National Pollutant Discharge Elimination System (NPDES) municipal stormwater permits in Washington State.

The Phase II permit authorizes the discharge of stormwater to surface waters and to groundwaters of the state from municipal separate storm sewer systems (MS4) owned or operated by the permittee (city of Aberdeen). The city is required to reduce the discharge of pollutants to the maximum extent practicable (MEP) and use all known, available, and reasonable methods of prevention, control and treatment (AKART) to prevent and control pollution of waters of the state of Washington.