Pollution of sediments and water bodies with toxic elements around the San Antonio-El Triunfo mining district, Baja California Sur, México is probably sourced from the tailings of abandoned mines that are hosted in mineralized Cretaceous granitoids. However, there is evidence to suggest local hot springs related to recent faults may be an additional source for contamination in the area. In this study, lead isotope signatures are applied to draw conclusions with regard to potential sources of toxic elements. Lead isotope ratios were analyzed from sulfides and scoria from the abandoned mines, fluvial sediments, and igneous rocks with secondary disseminated mineralization. To differentiate between superposed secondary and residual primary lead, leaching experiments were performed, and both leachate and residues were analyzed separately. Most of the residues from sediment samples have lead isotope ratios similar to those from the sulfides and scoria of the mining district, indicating that most of the lead in the detritus is related to the mineralized plutons. However, there is evidence of an additional detrital component. Lead isotope ratios from the leachates indicate a different source for the superimposed lead that is best explained by the contamination with the average Mexican industrial lead. Secondary disseminated mineralization that is related to younger, deep structures (hot springs) has different lead isotope ratios compared to massive vein sulfides and accounts for a significant amount in areas with high contamination levels. Thus, lead isotope systematics is a feasible method for tracing sources of toxic elements to distinguish between different natural, metallurgical, and anthropogenic inputs.