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The sediment microbial community plays a key role in the cycling of organic matter in marine ecosystems. The characteristics of the sediment microbial community are significantly related to changes in the environment. In this study, we analyzed the diversity and distribution of microbial communities in sediments from different geographical regions (the Liao River estuary, Yellow River estuary, hypoxic zone, and offshore zone) of the Bohai Sea using high-throughput sequencing. The results showed that the community richness and diversity (especially the unique diversity) of the Liao River estuary were larger than those of the Yellow River estuary, hypoxic zone, and offshore zone. The phylum <i>Proteobacteria</i> dominated in the Liao River estuary (46.26%), hypoxic zone (76.19%), and offshore zone (69.79%), while the dominant phylum in the Yellow River estuary was the <i>Bacteroidetes</i> phylum. The genus <i>Gillisia</i> was the dominant genus in both the Liao River estuary and Yellow River estuary. The offshore zone and hypoxic zone shared the same dominant <i>Photobacterium</i> genus. The results of Pearson correlation and redundancy analysis showed that environmental parameters such as nitrite, silicate, nitrate, phosphate, ammonia, dissolved oxygen, pH, and salinity interfered significantly with the structure and diversity of the microbial community. The results of this study will provide support for future research on the interaction mechanism of pollutants and microorganisms in the estuaries and a typical hypoxic zone of the Bohai Sea.