Abstract: The natural balance system of deep groundwater is disturbed by coal mining and drainage depressurization, leading to temporal and spatial changes in microbial communities in different aquifers. Herein, groundwater samples of Permian coal measures sandstone aquifer and Carboniferous Taiyuan Formation limestone aquifer with depths of 600 and 750 m are collected from the mine hydrological holes in Huaibei coalfield, and 16S rRNA gene V4 region sequencing method is used to test and analyze the microbial community diversity of deep groundwater. The operational taxonomic units (OTUs) numbers of coal measure water and Taiyuan limestone water samples range from 968−3071 and 820−3894, respectively, with the average values being 1980.43 and 1847.81 respectively. ACE, Shannon and Chao values show that coal measure water > Taiyuan limestone water. Simpson index shows that coal measure water < Taiyuan limestone water, indicating that coal measure water > Taiyuan limestone water, regarding the diversity of microbial community composition in groundwater. Main dominant bacteria phylum in Taiyuan limestone water and coal measure water are Proteobacteria, Bacteroidota and Planctomycetota; their relative abundance ranging 41.48%−97.36%, 0.57%–48.01%, 0.13%–15.29%, respectively. Main dominant bacteria genera in coal measure water are Thiovirga, Hydrogenophaga, and Flavobacterium; their relative abundance accounting for 5.98%, 4.39% and 3.43%, respectively of the total bacteria in the coal measure water. Hydrogenopaga, Acinetobacter and Thiobacillus are the main dominant bacteria genera in Taiyuan limestone water, their relative abundance being 11.13%, 4.72% and 4.40% respectively. Unique OTUs in coal measure and Taiyuan limestone aquifers number 1759 and 4107, respectively. F⁻, K⁺ and ORP are the main environmental factors affecting the bacterial community in groundwater. K⁺ impacts the abundance of the bacterial community in the Taiyuan limestone water to a greater extent than that of coal measure water. Contrarily, F⁻ affects the bacterial community in the coal measure water and Taiyuan limestone water is similar. As the aquifer depth increases, so does the influence of F⁻ and K⁺ on the microbial community abundance. The increase of F⁻ concentration of typical pollutants in Huaibei Coal strengthens some bacterial communities, resulting in changes in microbial community composition. The groundwater pollution caused by coal mining also enriches Thiothrix in the ash water. Huaibei coal measure water and Taihui limestone water are the main water filling sources for coal mining in Huaibei coalfield. Knowledge of the deep underground of the coalfield and how different water microbial community change, has been improved by this work, thereby providing a new method for identifying the water source of coal mine gushing (outburst), and a guarantee for the prevention and control of water disasters in coal mines.