This research investigated whether environmental conditions, biological fish characteristics and anthropogenic impacts influenced mercury (Hg) assimilation into the muscle tissue of two fish species from two Brazilian bays, Ilha Grande Bay and Guanabara Bay. Fish and superficial water were collected in different periods. Hg was determined by CV-AAS. Methylmercury (MeHg) was identified and quantified by ECD-GC. Chlorophyll a concentrations in the water column indicated that Ilha Grande Bay and Guanabara Bay were oligotrophic and eutrophic, respectively. Hg in fish ranged from 2.10 to 870.17 μg kg(-1) dry wt. in Ilha Grande Bay and 40.90 to 809.24 μg kg(-1) dry wt. in Guanabara Bay. Slight differences were found between the length-normalized Hg concentrations and its percent of Hg in a voracious predator from the bays. In Guanabara Bay, where the presence of a chlor-alkali plant causes Hg input, the iliophagous fish species showed the highest length-normalized Hg concentrations and the voracious predator the lowest. Iliophagous fish is consumed by voracious predator and, consequently, acts as their MeHg food supply. Iliophagous fish from Ilha Grande Bay presented a higher percent of MeHg (80.0 %) than specimens from Guanabara Bay (54.5 %). This fact suggests that more MeHg was transferred from iliophagous fish to voracious predator in Ilha Grande Bay. At Guanabara Bay, the bioproduction is greater than that at Ilha Grande Bay, presenting the highest biomass in it ecosystem, which may subsequently dilute Hg and reduce its availability to the biota; i.e., influencing in Hg and MeHg availability throughout the food chain. Consequently, more MeHg is available in the aquatic environment of Ilha Grande Bay.