The paper estimates the epidemic value of indicators for microbial contamination of waters from their main supply sources (waters from the Tsimlyansk Reservoir and the Nizhni Don River and drinking waters from the towns of Azov and Tsimlyansk) in the Rostov Region. The Tsimlyansk Reservoir water met the SanPiN 2.1.5.980-00 requirements for the normalizable indices of total coliform bacteria (TCB) and thermotolerant coliform bacteria (TtCB) in 54% of the samples; glucose-positive coliform bacteria (GPCB) and Salmonella were isolated in 100 and 60%, respectively. The Azov drinking water that met the SanPiN 2.1.4.1074-01 requirements for TCB and TtCB) was found to contain GPCB, Klebsiella, and Pseudomonas aeruginosa in 5.7, 4.8, and 3% of the samples, respectively Direct detection of pathogenic and potentially pathogenic microorganisms and the integral GPCB index are of the greatest prognostic value in assessing a microbial risk for waterborne enteric infections.