The comparison of biochemical, morphological and genotoxic responses sampled from areas protected from cronic or acute contamination with responses of organisms sampled from historically contaminated areas is useful in determining the environmental quality of ecosystems. This study aimed to analyse biomarker responses using Mugil liza (mullets), Geophagus brasiliensis (acaras) and Tilapia rendalli (tilapias). The fish were sampled from the Rodrigo de Freitas Lagoon, Magé (Ipiranga beach and Olaria), São Gonçalo (Gradim), Itaipu and Jacarepaguá Lagoon. At the laboratory, morfometric measurements were taken, in order to calculate the Gonadossomatic Index (GSI), Hepatossomatic (HSI) and Condition Factor (CF). Mullet brains were removed to obtain Acetilcolinesterase, which was then exposed to standard-solutions of polycylic aromatic hydrocarbons (PAH), to verify the influence these compounds might have on the activity of the Acetilcolinesterase enzyme. The fish bile was removed to determine metals and billiverdin concentrations. Livers and gonads were removed to conduct hystopathological analyses. Results indicated no correlation between the GSI and HSI. Preliminary data on the AChE activity in the presence of HPA were not conclusive. The fish bile analysis regarding metals demonstrated the presence of Nickel, Selenium, Arsenium and Chrome in the bile of the species Mugil liza, both from Ipiranga beach and Itaipu. Billiverdin concentrations did not present significant relationship with HPA concentration, as suggested by some authors. The hystopathological analyses indicated more cellular abnormalities in fish sampled from Magé than in Itaipu, with the presence of higher than normal number of melanomacrophages, leucocitary inflitrations and parasites.