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As with most countries in transition, sewerage system development lags far behind water supply systems. There is no wastewater treatment system; sewerage is dispersed into open areas. The first urban wastewater treatment plant constructed in Skenderaj is not yet fully operational. Sewerage services are under the direct jurisdiction of the seven RWCs. The present wastewater management in Kosovo covers the collection of the wastewater and storm water out of the settlement area and the discharge of these flows untreated into the nearest river. Only approximately 30% of Kosovo?s population have access to a sanitation system, including less than 10% of the rural population; the rest have, at best, septic holes. In the absence of a sewage network, the population tend to be self-providers, limited to simple cesspools, latrines or septic tanks. Access to sewerage disposal appears unrelated to ethnicity; 71% of Kosovo Albanians, 69% of Kosovo Serbs and 80% of other minorities reportedly have access (UNDP and USAID, 2009).http://waterwiki.net/index.php/Image:Figure1SanitationCoverageKosovo.jpg
There is no system for monitoring sewage discharge and treatment of municipal wastewater is virtually non-existent, with the exception of some septic tanks for restricted housing areas or natural ponds, which have been formed at the discharge points of wastewater collection systems. A few Kosovo Force (KFOR) camps and the hospital complex of Pristina have biological treatment plants.

Untreated sewage discharge represents a major source of pollution of natural waters, affecting dissolved oxygen, phosphorous and nitrogen content, and pathogenic bacteria and viruses. The main surface water polluters are municipalities and industries. Municipalities and communities discharge wastewater without any treatment, reducing water quality. Industrial activities decreased dramatically during the Kosovo war (1998-1999), but the existing industrial plants do not have any kind of wastewater treatment. Mining and metallurgical industries are the biggest culprits, emitting heavy metals into the water. Data on wastewater discharges from each municipality are summarised in Annex 1.

The absolute absence of any experience, tradition and basic knowledge on biological treatment processes (knowledge about wastewater treatment technology is restricted to septic tanks with preceding disinfection by chlorination) is the base situation from which the introduction of wastewater treatment has to start. Based on best available data, the total wastewater discharge in 2004 in Kosovo is about 1,200 l/s or 110,000 m3/d. The BOD and solids loads are 8,500 kg/d and 29,000 kg/d, respectively.

Due to water contamination and unsafe hygiene (hand washing at critical times, unsafe handling, transportation and storing of drinking water), waterborne diseases are widespread among rural populations. Improvements have been made in urban areas; water contamination has reduced to 10% on average, but remains a big issue in Shtërpcë and Klina. Klina had 28 cases of typhoid in 2008 and 42 of Hepatitis A. No reliable scientific data portrays the level of infection of children and adults by waterborne diseases.