The microbiological contamination of the water in the Black Sea basin is a direct effect of both natural and anthropogenic causes. The increase in nutrient and pollutant loads comes from rivers, such as the Danube, from industrial and municipal wastewater sources along the coast and from discharges into the sea. Thus, the Danube provides majority of the river inflow to the Black Sea and changes within the river basin are having effect on the presence and evolution of nutrients and pollutants in the sea. Due to the fact that a crucial issue throughout the rivers and especially in the Danube and Black Sea basin is the microbiological contamination with faecal bacteria resulted from anthropogenic activity, the assessment of the presence of pathogenic bacteria in water is a major concern for the protection of human and animal health. Coliform bacteria are indicators for the assessment of faecal pollution and a potential presence of pathogens, which is caused mainly of untreated wastewater. In this study the rate of the microbiological contamination of the Black Sea and Northern Aegean Sea water collected in the BSB27 MONITOX project target sites, from SE part of Romania and NE part of Greece, was evaluated by counting of the bacteria indicators of the organic pollution (heterotrophic bacteria and the total coliforms). Total mesophilic aerobic bacteria from the analyzed water for Black Sea area (Romania), ranged from 1.11 x 10² to 1.70 x 104 CFU/mL and MPN of coliforms between 250 CFU/mL to 7000 CFU/mL. For area of Aegean Sea (Kavala, Greece) the MPN of coliforms were absent and the number of mesophillic aerobic bacteria was 1.50 x 10 CFU/mL.