Arsenic and mercury are among the metals and metalloids more toxic to the ecosystem. A quantification method by atomic absorption spectroscopy with hydride generator (AAS-HG) to determine total As and cold steam to determine Hg was optimized and validated in various matrices: superficial water, interstitial or pore water, sediments and in gill, liver and muscle of two fish species, a silverside (Basilichthys microlepidotus) and a catfish (Trichomycterus areolatus). The quality of the results was tested using certified reference materials (Water: ERM-CA615; Fish: DOLT-4; Sediment: BCR-320R). Samples were collected in the affluent and effluent of five reservoirs: Cogotí (31º00'S, 71º05'W); Corrales (31º54ºS, 70º54'W); La Paloma (30º44'S, 71º00'W); Rapel (34º08'S, 71º29'O); Recoleta (30º28'S, 71º06'W). ), in two campaigns during high flow (winter 2010) and low flow (summer 2011).The results show a clear difference in the distribution of As and Hg in the different matrices; higher concentrations were found in the order sediment ˃ interstitial water ˃ surface water. Catfish showed higher accumulation of both metals, and metal concentrations generally decreased in the order liver > gill > muscle. No significant effect of reservoirs and zones was observed in As and Hg content. However, Arsenic (As) was found in higher concentration in the different matrices of the five reservoirs and zones. The concentrations of As and Hg in all samples did not exceed international standards in the case of sediment and the Chilean norm in the case of water, while in both fish species concentrations of As and Hg in muscle exceeded international standards.