During January 2013, a mining spill occurred in the Santa Maria mining region, releasing around 300,000 m3 of tailings on Los Remedios river, which was transported through the San Lorenzo river and finally to El Comedero (EC) dam. Twenty months later, we examined the concentrations of Hg and Se in the muscle, liver, gills, and guts of three fish species (Cyprinus carpio, Oreochromis aureus, Micropterus salmoides) captured in the EC dam to assess the performance of the cleaning operations. A high Se concentration in the liver of all species (carp, 1.2 ± 0.4; tilapia, 3.9 ± 2.1; bass, 3.5 ± 1.1 µg g−1 ww) was consistently observed, while this behavior was only found in the blue tilapia for Hg (0.15 ± 0.11 µg g−1 ww). Tilapia (benthic-detritivorous) exhibited the highest Se concentrations compared to the carp (omnivore) and the largemouth bass (piscivore). In contrast, the largemouth bass had the highest Hg levels in the muscle compared with the other fishes. Such differences could be related to the different metabolism and feeding habits among species. Compared to a tilapia study carried out three months after the mine spill during a mortality event, a decrease was evident in the liver for Se and Hg by 7.2 and 4.7 times, respectively. This reveals that cleaning operations were more efficient for Se and less for Hg, and that a prolonged period was required for the partial recovery of the element levels in fish from sites impacted by mining. Considering the Mexican consumption scenarios for each fish species, it could be concluded that there will be no non-cancer risk by exposure to Hg or Se.