Guanabara Bay, in Rio de Janeiro state, is impacted by organic matter, oil and heavy metals. The present study evaluated the total mercury (THg) and methylmercury (MeHg) concentrations and the MeHg to THg ratio (%MeHg) in water samples from different points of the bay and in 245 organisms of three different trophic levels sampled between 1990 and 2000. Dissolved mercury concentration in estuarine water samples ranged from 0.72 to 5.23 ngl(-1). THg and MeHg in mussel, ranging from 11.6 to 53.5 microg THg kg(-1) wet wt. and 4.5-21.0 microg MeHg kg(-1) wet wt., varied according to sampling point and water quality. Planktivorous fish and mussel presented similar MeHg concentrations, meanwhile THg in planktivorous fish were lower than in mussel. Carnivorous fish showed higher THg and MeHg concentrations (199.5 +/- 119.3, 194.7 +/- 112.7 microg kg(-1) wet wt. respectively) than organisms from other feeding habits and lower trophic levels. There was a significant difference in the %MeHg among trophic levels: mussel presented lower MeHg percentage (33%) than planktivorous fish (54%) and carnivorous fish (98%).