Discharges of pollutants or other wastes that require permits from the department under RCW 90.48.160, which are not satisfied through permits issued under this chapter, shall be subject to the permit requirements of RCW 90.48.160, et seq. Except where permits under RCW 90.48.160 are issued by a municipal corporation pursuant to chapter 173-208 WAC, permit requirements under this chapter and permit requirements under RCW 90.48.160 shall be contained in a single permit document.