▸ The δ13C and δ15N findings showed different trophic relationship in food webs from Rio de Janeiro bays. ▸ Guanabara Bay showed depleted δ15N values compared to Sepetiba and Ilha Grande bays. ▸ Ilha Grande Bay showed significant depleted δ13C values. ▸ Our findings indicate THg biomagnifications up food webs in Rio de Janeiro bays. ▸ Ilha Grande Bay food web showed the highest trophic magnification factor. The present study investigated trophic relationships and mercury flow through food webs of three tropical coastal ecosystems: Guanabara, Sepetiba and Ilha Grande bays. The investigation was carried out through carbon and nitrogen stable isotopes (δ13C, δ15N) and total mercury (THg) determination in muscle from 35 species, including crustacean, cephalopod, fish and dolphin species. Detritivorous species showed the lowest average δ15N values in all bays. These species were 13C enriched in Sepetiba and Ilha Grande bays, suggesting the presence of 13C enriched macroalgae in their diet. The highest mean δ15N values were found in fish and benthic invertebrate feeders, as well as in species presenting demerso-pelagic feeding habit. The carbon and nitrogen isotopic findings showed different trophic relationship in food webs from Sepetiba, Guanabara and Ilha Grande bays. Guanabara Bay showed to be depleted in δ15N compared to both Sepetiba and Ilha Grande bays. The latter finding suggests substantial contribution of atmospheric nitrogen fixation by cyanobacteria. A positive linear relationship was found between logTHg concentrations and δ15N values for Guanabara and Ilha Grande bays, but not for Sepetiba Bay. Our findings showed trophic magnification factors (TMF) above 1, demonstrating that THg is being biomagnified up the food chains in Rio de Janeiro bays.