To study the distribution features of microorganisms in distinct hydrological areas of the southern Qinshui Basin, C-N-S microorganisms were studied using 16S RNA sequencing, metagenome sequencing and geochemical technologies, showing the high sensitivity of microorganisms to the hydrodynamic dynamics of coal. The hydrodynamic intensity of the #3 coal gradually decreased from the runoff areas to the stagnant areas. The stagnant zones have higher reservoir pressure, methane content, δ13CDIC and TDS and lower SO42-, Fe3+ and NO3- concentrations than the runoff areas. C-N-S-cycling microorganisms, including those engaged in methanogenesis, nitrate respiration, fermentation, nitrate reduction, dark oxidation of sulfur compounds, sulfate respiration, iron respiration, chlorate reduction, aromatic compound degradation, denitrification, ammonification and nitrogen fixation, were more abundant in the stagnant areas. The relative abundance of C-N-S functional genes, including genes related to C metabolism (e.g., mcr, mer, mtr, fwd and mtd), N metabolism (e.g., nifDKH, nirK, narGHI, nosZ, amoB, norC and napAB) and sulfur metabolism (e.g., dsrAB and PAPSS), increased in the stagnant zones, indicating that there was active microbiological C-N-S cycling in the stagnant areas. The degradation and fermentation of terrestrial plant organic carbon and coal seam organic matter could provide substrates for methanogens, while nitrogen fixation and nitrification can provide nitrogen for methanogens, which are all favorable factors for stronger methanogenesis in stagnant areas. The coal in the study area is currently in the secondary biogenic gas generation stage because of the rising of the strata, which recharges atmospheric precipitation. The random forest model shows that the abundance of C-N-S microorganisms and genes could be used to distinguish different hydrological zones in coal reservoirs. Since stagnant zones are usually high-gas-bearing zones and high-production areas of CBM exploration, these microbiological indicators can be used as effective parameters to identify high-production-potential zones. In addition, nitrate respiration and sulfate respiration microorganisms consumed NO3- and SO42-, causing a decrease in the content of these two ions in the stagnant areas.