There are two water treatment plants in the Lake Ohrid basin. Approximately 44,000 inhabitants are not connected to the drainage system, including several larger villages located on the Lake's shore. The effluent from these settlements flows, directly or indirectly, into the Lake. The water treated in the protection system of the Lake is discharged into the river Crn Drim that flows out the Lake.

Municipal waste water is accumulated in secondary collecting systems, a special sewage system. These collection systems are managed by public water companies. Since 1988 the secondary collection systems redirects the accumulated waste water to the primary collection system. Certain parts of the city of Ohrid, due to lack of funds for the construction of a comprehensive secondary system, have not yet been connected to the primary collection system. In the primary collection system the water is pumped out and carried into the treatment plant near the village Vranista (Struga) via pump stations.

At present, approximately 20,000 inhabitants of Ohrid and 14,000 of Struga are connected to the Vranista treatment plant. The capacity of the waste water treatment plant is for 120,000 inhabitants. At present two thirds of the plant's capacity are operational during tourist season, and only one third in the rest of the year.

Hotels located on the shore of Lake Ohrid that are not connected to the sewage system have their own facilities for prior eliminating treatment.

There are no water treatment plants in Albania. Along the shore only the town of Pogradec has a waste water collection system for approximately 30 - 40% of its inhabitants. The entire system is poorly maintained and in a bad state. In the area that is not connected to the collection system the method of infiltration into the soil or into the water of the rivers flowing into the Lake has been used. Thus, the effluent of about 36,000 inhabitants from the Albanian shore, directly or indirectly, are discharged into the Lake.

In recent years Lake Ohrid has been intensely monitored in terms of financing its protection. For this purpose, the World Bank has approved and given its consent for funding a Project for Protection of the Lake that includes both Macedonian and Albanian counterparts.