Data on the abundance of heterotrophic bacterioplankton and bacteriobenthos in the northern and middle parts of the Caspian during the period from 2013 to 2017 are presented. In the waters of the northern part of the Caspian, a peak in the number of saprotrophs and crude oil degraders was recorded in 2013. In the middle part of the Caspian and in the region of the Mangyshlak regression, high numbers of heterotrophic bacteria were recorded in 2013 and 2016. The biodiversity of bacterioplankton in the surveyed areas is almost the same; the species composition of saprotrophs and crude oil degraders is identical. In the bottom sediments of the northern and middle parts of the Caspian Sea, two peaks of saprotrophic bacteriobenthos development (in 2013 and 2016) were recorded; in the region of the Mangyshlak threshold, the concentration of saprotrophs remained stable. The number of crude oil degraders was inferior to those of saprotrophs, while the proportion of crude oil degraders to saprotrophs changed annually. The species composition of saprotrophs is relatively stable, the biodiversity of oil-oxidizing bacteriobenthos has changed in the direction of increasing the proportion of non-fermenting bacteria. Constant changes in the ratio of the number of saprotrophs and crude oil degraders, together with the transformations of the dominant groups of the species composition of bacteria, indicated the instability of bacteriobenthos, and, as a result, the vulnerability of the microecosystem of bottom sediments under changing environmental conditions.