This study explores the hydrochemistry and microbial communities in groundwater from mining areas and their environmental responses. We took a mining area in Erdos, Inner Mongolia as example for analysis, where 23 samples were collected from groundwater in different aquifers, water accumulated in the mined-out area, and roof water to conduct hydrochemical analysis and 16S rDNA high-throughput gene sequencing. Results show that groundwater in different aquifers varied considerably in their hydrochemical types: water samples from the Quaternary and Cretaceous systems were mainly of HCO₃-Ca·Mg and HCO₃-Na types, while those from the Jurassic system and mined-out areas were of SO₄-Na type. Quaternary groundwater exhibited the highest microbial community diversity, a dominant functional bacterial community was formed in water accumulated in the mined-out area due to human disturbance. Jurassic and Cretaceous groundwater showed lower microbial community diversity as they were limited by permeability and redox conditions. 64 phyla and 1,294 genera of microorganisms were identified: Proteobacteria (63.47%-85.15%) was the dominant bacterial group, Desulfobacterota (1.90%-5.80%) was enriched in deep groundwater, and Actinobacteriota (1.70%-4.50%) showed higher abundance in shallow groundwater. Water samples from the Jurassic system and mined-out areas shared 53 common genera, revealing hydraulic connections and pollution diffusion pathways. This indicated the source of water filling, and the highest number of unique genera (145 species), reflecting the significant disturbance of mining activities on microbial ecology. 11 environmental factors, including pH, NH₄⁺, and K⁺, significantly influenced the community structure. Groundwater microbial communities showed significantly different response mechanisms to hydrochemical characteristics across different aquifers, reflecting the dominant role of hydrogeological background and types in the aquifers. The microbial community in the water accumulated in the mined-out area interacted most strongly with environmental factors, confirming that mining activities exacerbated the coupling effect between the environment and microorganisms. This study combines microbial community research with hydrological environmental indicators, offering new insights into the microbial ecological functions in the underground aquifer system of mining areas and the groundwater environment in mining-disturbed areas. This study provides references for groundwater source identification, pollution traceability, and microbial ecological restoration research in mining areas.