The mineralization of benzene, toluene, ethylbenzene, and xylene (BTEX) into inorganic substances by microorganisms may affect the water–rock interaction. However, few studies have quantitatively analyzed the processes. To quantitatively reveal this mechanism, in this study, nitrate and toluene were taken as the typical electron acceptor and BTEX, respectively. Based on hydro-geochemical theory, the mechanism and mathematical model were established. In addition, the model was verified with a toluene mineralization experiment. The mechanism model demonstrated that H+ was the main factor in the dissolution or precipitation of CaCO3. The mathematical model derived the equations quantitatively between the amount of toluene mineralization, CaCO3, and some biogeochemical indicators, including temperature, microbial consumption, and other major ions in groundwater. According to the model, the amount of dissolved CaCO3 increased with the increasing proportion of completely reduced nitrate. For a complete reaction, the greater the microorganisms’ consumption of toluene was, the smaller the precipitation of CaCO3. CaCO3 dissolution was a nonmonotonic function that varied with temperature and the milligram equivalent of other ions. Furthermore, the validation experiments agreed well with the mathematical model, indicating its practicality. The established model provides a tool for assessing the biodegradation of toluene by monitoring the concentration of groundwater ions.