The paper presents the results of study of the Prut River heterotrophic bacterioplankton. The bi-disciplinary technique was used to assess its hydrocarbon-oxidizing activity, namely: microbiological research was carried out in parallel with hydrochemical investigation of the natural water samples and samples enriched with diesel fuel. The Moldovan-Romanian transboundary section of the Prut River includes various ecological zones, such as the Costești-Stanca Reservoir, the mouth of the Jijia River, the Prut floodplains with the relict Beleu Lake (where oil extraction is carried out despite the fact that it is a protected area of the scientific reserve "Prutul de Jos") and the Prut River mouth with the Giurgiulesti International Free Port. The microbial community of fluvial bacterioplankton corresponds to the specific conditions of each these biotopes, being the most reproducible and adaptable component of the biota. The results obtained in the study of the Prut River bacterioplankton demonstrate the presence of hydrocarbon-adapted microorganisms with a good potential to utilize petroleum products in their metabolic processes.