A hydrogeochemical and isotopic study was conducted in the western portion of the Celaya Valley Aquifer, Mexico, to assess the role of dissolved carbon dioxide in groundwater contamination. The partial pressure of carbon dioxide value is used to evaluate a complex hydrogeochemical environment, and the carbon dioxide behavior is used to identify the natural and anthropogenic processes related to pollution sources in a thermal aquifer located in the western portion of the Celaya Valley Aquifer. Results indicate that during groundwater migration from the recharge zone to the center of the basin, a hydrogeochemical evolution from calcium bicarbonated and calcium–bicarbonate–chloride type to sodium–bicarbonate type occurs. During this process, deep fluids that migrate through the fault system interact with the aquifer; these fluids contain carbon dioxide released from the metamorphism of the carbonated basement, although another source is not discarded as the dissolved inorganic carbon typical of meteoric groundwater produced from atmospheric carbon dioxide. The hydrogeochemical and isotopic evidences of delta carbon thirteen, delta oxygen eighteen and delta deuterium indicate that the dissolved content of carbon dioxide in the aquifer is involved in the silicate weathering process that plays a major role during water type evolution. In some cases, during weathering, potentially toxic elements are released in amounts that represent an environmental risk, among which arsenic and fluoride stand out, mainly in depth wells. Additionally, other isotopic and hydrogeochemical evidence indicates a biological source of carbon dioxide in the shallow aquifer, primarily due to the agricultural activity carried out in the entire study area. Graphic abstract