We developed a multicomponent, 1D advective transport model that describes the downgradient evolution of solute concentrations, ⁸⁷Sr/⁸⁶Sr ratios, and δ¹¹B values in the Wyodak-Anderson Coal Bed (WACB) aquifer located in the Powder River Basin, Wyoming, USA. The purpose of the study was to evaluate the chemical vulnerability of groundwater to potential environmental change stemming from the extraction of coal bed methane and shale gas. Model calculations demonstrate that coupling between microbial activity and the dissolved carbonate system controls major ion transport in the WACB aquifer. The analysis of ⁸⁷Sr/⁸⁶Sr ratios further reveals the importance of ion-exchange reactions. Similarly, δ¹¹B data emphasize the significance of pH-dependent surface reactions and demonstrate the vulnerability of the aquifer to the long-term acidification of recharge water.