Trace elements As, Co, Fe, Hg, Se, Zn and Cr were determined in muscle tissue, gills and liver and nuclear abnormalities in erythrocytes (NAEs) were observed in 7 fish species (Chaetodipterusfaber, Paralanchurusbrasiliensis, Micropogoniasfurnieri, Achiruslineatus, Genyatremusluteus, Menticirrhus Americanos and Micropogoniasfurnieri), from two estuarine regions subject to different levels of anthropogenic impact (preserved and polluted) to provide information on contamination levels. The bioaccumulation in C. faber suggested that it should be proposed as a bioindicator of pollution in estuaries. The hydrological data: temperature, salinity and dissolved oxygen characterized the estuarine waters. A paradoxical result relating to As, Co, Fe and Zn concentrations was that, in general, these were higher in the fish species of the Cananeia estuary (a preserved area), while Hg concentrations and NAEs were higher in the species of the Santos-SĂŁo Vicente estuary (SSV) (the polluted area). The bioaccumulation in tissue-organs decreased in the following order: liver>gill>muscle, with the exception of Hg that was liver>muscle with no detection in gills. Concerning the genotoxic effects, C. faber showed a more significant NAE, besides clastogenic effects, demonstrated by the greater frequency of micronuclei. Differences found between the fish species could be related to their feeding habits and to salinity. This is a contribution to making fishery efforts more profitable and enhancing the bioindicator bank.