Coalbed methane is a major unconventional resource that has been exploited commercially for decades in the southern Qinshui Basin of China. The hydrogeochemical characteristics of coal reservoir water play a key role in the exploration and development of coalbed methane resources. In view of this, a detailed study was performed on coalbed methane co-produced water collected from the Shizhuangnan block to assess water–rock interactions and biogeochemical processes. Water samples were analyzed to establish major ions, isotopic compositions and perform 16S rRNA sequencing. Results suggest that the hydrochemistry was controlled by water–rock processes and that methane was consumed by sulfate reduction through calculation. Meanwhile, the isotopic compositions of water samples indicated that they had a predominantly meteoric origin and were influenced by microbial activity. The 16S rRNA sequencing results of bacteria and archaea provide an important foundation for understanding the activity of sulfate-reducing bacteria and methanogens at different hydraulic heads, which was consistent with isotopic analysis. Carbonates containing calcite and dolomite were found to be distributed at different hydraulic head due to the biogeochemical characteristics and associated water–rock interactions.