Objective Prolonged exposure to heavy metals, such as Pb, Hg, or Cu, has multiple adverse effects on marine organisms at the cellular, physiological, and population levels. Bivalves' histopathology provides a sensitive biomarker of pollutant‐induced stress and environmental health. Gonad tissue deterioration is of particular concern, as it affects the reproductive success of a species. This study aimed to examine the histopathological alterations caused by metal exposure in the gonad of the white clam Dosinia ponderosa. Methods Organisms were sampled from three locations in the Gulf of California: Santa Rosalia (SR), a former Cu mining town; San Lucas beach (SL), a nearby site influenced by pollution; and Escondida beach (EB), which served as a control site. Histological and histochemical stains were used, and the prevalence and intensity level of each alteration were calculated. Result The prevalence of alterations was higher in the ovaries of SR clams (92% compared to 60% in SL clams and 32.7% in EB clams), during spawning (91.4% compared to 20% in SL clams and 4.7% in EB clams), and in winter (93.5% compared to 30% in SL clams and 17.4% in EB clams). Conclusion These findings suggest a significant deterioration in the gonads of white clams from SR, probably linked to the chronic exposure to high concentrations of Cu and possibly other heavy metals; hence, the reproductive health of the clams is likely compromised. Impact statement This research provides evidence of the adverse impact of the mining industry on marine organisms, when mining waste is transported to the sea by natural runoff. These results also have implications for human health, since the clams studied in this research are part of the regional diet.