This paper analyzes regional hydrogeological conditions and divides the study area into three hydrogeological types and seven hydrogeological units, to investigate hydrogeology and its effect on coalbed methane (CBM) enrichment in the southern Junggar Basin, China. From this work, it is found that the groundwater flow paths in the study area are the joint effects of south-to-north and west-to-east flows. This study also shows that microbial gases are widely developed, although the depth limit of microbial gas occurrence is still unclear in the study area. Microbial CO2 reduction is the leading formation path in the study area, except for the Houxia region, where fermentation is the formation mechanism. The abnormally high CO2 in stagnant zones (i.e., water flow is slow and stagnant) is mainly associated with methanogenesis, whereas relatively low CO2 (microbial or thermogenic) is present where water flow is active. The average CBM content within the Xishanyao Formation changes within various hydrogeological units; moreover, the average CBM content within the Badaowan Formation of the same hydrogeological unit (e.g., Fukang) suggests that the hydrogeological and CBM enrichment conditions are different within various structural types. Overall, the hydrogeological conditions exert control on the gas content in the study area; that is, the gas content is high in stagnant zones. Finally, influenced by supplemental microbial gases, changes in the CBM oxidation zone are relatively complex in the study area, the depth of which has no obvious correlation with hydrogeological conditions and changes significantly from west to east.