Chapala, the largest lake in Mexico, has a great potential for aquaculture and a community of some 2500 fishermen who are interested in this activity. However, diverse reports over the past two decades suggest that the fish there are contaminated with heavy metals, raising concern among consumers. Although more recent scientific studies have clarified that the metal content in the edible parts of fish is below allowable limits, the negative perception persists. The present study, therefore, was designed to evaluate the bioaccumulation of the metals Cu, Zn, Pb, As, and Cd in organs such as the muscles, liver, and gills of carp (Cyprinus carpio) cultured in Lake Chapala, and compared the results to fish cultured in a pond. Results after 473 days of monitoring showed that metal bioaccumulation in the muscles of the carp increased by 1.71, 0.50, and 12.36 μg/kg for Cu, Cd, and Pb, respectively, but Zn and As levels decreased by 7.84 and 131.7 μg/kg, respectively. The livers showed concentrations one or two times higher than the muscles in the case of Pb, Cu, Zn, and Cd. According to these results, the metal concentrations in the edible parts of these fish were below international standards for human consumption, and no significant differences were found between the bioaccumulation patterns in the muscles and livers of the carp cultured in the lake and those raised in the pond, except for Cd and Pb in the liver. Finally, no correlations were found between metal concentrations in the fish and lake sediments.