The failure of a tailings dam occurred in January 2013 at the Santa María de Otáez mining region (Mexico) released a spill (~ 300,000 m3) on Los Remedios River, which was transported through the San Lorenzo River, and finally to El Comedero (EC) dam. The concentrations of metal(loid)s in the muscle, liver, gills, and guts of three fish species (Cyprinus carpio,Oreochromis aureus,Micropterus salmoides) collected from EC dam were examined twenty months later to assess the performance of the cleaning operations. The bioaccumulation patterns of the metal(loid)s in the tissues were different in the three fish species. Tilapia had the highest Cd (11.23 ± 8.53 µg g−1) and Cu (871 ± 1261 µg g−1) concentrations in the liver, as well as As concentration (83.6 ± 61.7 µg g−1) in the gut, while the highest Zn concentration (745 ± 356 µg g−1) was measured in the gills of the carp. Such variability can be caused by the variant bioavailability of the metal(loid)s and by the feeding habits of each species; and also by the fact that some metals are essential and better regulated by organisms than other non-essential. Compared to a study of tilapia carried out 90 days after mine spill, a decrease was evident in the liver for As, Cd, Cu, and Zn by 129, 5, 10, and 1.7 times, respectively. This revealed that cleaning operations were more efficient for As. The target hazard quotient and the hazard index were < 1, which indicates there will be no risk of consuming muscle in moderated rations of the three fish species.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10653-023-01509-8.