In the Aral Sea Basin, human activities have led to the severe degradation of water and soil, which is considered to cause serious human health problems. Epidemiological evidence, however, was lacking. This study investigates the microbiological contamination of drinking water in the Khorezm district in Uzbekistan as a case study in the Aral Sea Basin. The incidence of diarrheal diseases was monitored, and the risk factors water, sanitation and hygiene were studied using a combination of quantitative and qualitative methods. Recommendations for improved drinking water hygiene and sanitation are given.