In the two ports, the Ports Authority has outlets for rainwater, combined sewers, industrial waste, and post-dredged water outlets. All sewage and wastewater, the river Oder in Szczecin and river Swina in Swinoujscie, is subject to pre-treatment before in goes to the reception facilities.

Sanitary sewage from the major part of the port in Szczecin is discharged to the wastewater treatment plant Ostrow Grabowski. The operation of the plant is carried out by the water company "Miedzyodrze"http://www.miedzyodrze.pl/

The sanitary sewage from the area of the port of Swinoujscie is discharged to the municipal wastewater treatment plant in Swinoujscie and sewage treatment plant on the port’s territory, which is the operated by the Ports Authority.