An assessment of the current ecological state of Sivash Bay (southern part of the Eastern Sivash) under the conditions of changes in its water regime is given in this study. Judging from the concentrations of the main pollutant classes, the prevailing type of anthropogenic impact on the ecosystem state of the studied area is the reduction of freshwater runoff, which caused the growth of salinity. Quantitative indicators of the microbial community of the bay bottom sediments characterize their pollution with organic substances. The increase in salinity of the reservoir caused a restructuring of the main components of the bottom community, such as meio and macrozoobenthos, expressed in a lowering of the biodiversity indicators and a change in the biocenosis taxonomic structure.