This study assesses the concentration of total mercury (THg), methylmercury (MeHg) and the % MeHg in muscle tissue, liver and gonad of three fish species (Micropogonias furnieri - Atlantic croaker; carnivorous fish, Bagre spp. - Catfish; omnivorous fish and Mugil liza - mullet; planktivorous fish). Furthermore, some other biotic parameters with: total length, weight, age, sexual maturity and sex. The mercury concentration along the last thirteen years in Atlantic croaker and mullet muscle tissue was assessed. THg concentrations were determined by cold vapour AAS with sodium borohydride as a reducing agent. The MeHg was made by CG-ECD. Theses analytical methodologies presented high precision and accuracy when tested with certified reference materials from IAEA - MA-1 and DOLT 2. The carnivorous fish showed higher THg and MeHg concentrations in its muscles than omnivorous and planktivorous fish. The liver of all fish species showed higher THg concentrations than the muscle tissues and gonad. Meanwhile, the MeHg concentrations were higher in the muscle. Atlantic croaker presented higher percentage of MeHg in liver than catfish and mullet. The fish species showed similar percentage of MeHg in their gonad. Significant and positive correlations were observed between THg concentration in catfish muscle and their total length and weight. Mann-Whitney test showed that the stage of the life of the individuals was one of the parameters that influenced THg concentration in the muscle for carnivorous fish planktivorous fish. The results presented a statistically significant difference between the THg in the muscle of the organisms of the Atlantic croaker and the mullet collected in the years 1999 and 2003.