Mine wastes from the La Aurora mine in the state of Guanajuato were generated by the flotation process and placed in four tailing dumps on the local stream while the plant operated. Given that these wastes contain toxic elements, it is important to establish their impact on the quality of several surrounding natural sources of water that are considered potential drinking water supplies. This study identified four water source types, in which the contents of arsenic (As), mercury (Hg), and thallium (Tl) were exceeded, according to international guideline values for drinking water quality. The first type of aqueous sample corresponded to leachates produced by rainwater infiltration in tailings and water-mineral waste interactions. The second type corresponded to surface water along the Xichú and La Laja Streams, and the third and fourth types involved two groundwater well samples and spring samples, respectively. The Chiquito Stream was used as a reference area that had not been impacted by the mine wastes. The isotopic signatures associated with δ34Ssulfate and δ18Osulfate compositions from the El Ojo de Agua spring are similar to those of the Santa María River and are different from those of the mine waste leachates. This study shows evidence of the presence of As in the El Ojo de Agua spring, which results from dissolution of secondary mineral phases that were produced by alteration of the mine wastes, which then migrated along the Xichú Stream system until reaching the spring. These As-bearing fine particles are prone to dissolution when in contact with this water source. Principal component analysis revealed that the observed As, Tl, and Hg can be attributed to weathering of the mine wastes. However, the results suggest that a natural contribution of these elements could be associated with rainwater-igneous rock interactions.