In the presented article studied the microbiological regime of the transboundary rivers like as Araz and Ganikh in the territory of the Republic of Azerbaijan. In a country where up to 70% of its surface water resources are formed by transboundary rivers, these rivers, especially the Araz river, enter the territory of Azerbaijan in a biologically and chemically polluted state and the pollution continues throughout the country. In this case, the degree of pollution of these rivers across the country also differs from each other. Thus, while the pollution of the Ganikh River in Azerbaijan is weak, this process in the Araz River weakens somewhat after entering the country, but after a certain distance, the process continues along the entire course until it flows into the Kura River in an ascending line. The reasons for this different pollution are mainly related to the number of settlements along the river, the nature of river use, the lack of a centralized sewage system and so on.