- The study investigated trophic relationships and mercury biomagnification in three tropical coastal ecosystems: Guanabara, Sepetiba, and Ilha Grande bays.- Detritivorous species in all bays showed the lowest average nitrogen isotope values, suggesting their diet includes 13C-enriched macroalgae.- Fish and benthic invertebrate feeders, as well as species with demerso-pelagic feeding habits, had the highest nitrogen isotope values.- Carbon and nitrogen isotopic findings showed different trophic relationships in the food webs of the three bays, with - Guanabara Bay being depleted in nitrogen compared to Sepetiba and Ilha Grande bays.- A positive linear relationship was found between mercury concentrations and nitrogen isotope values in Guanabara and Ilha Grande bays, indicating biomagnification of mercury in the food chains.- Trophic magnification factors (TMF) above 1 were observed, demonstrating that mercury is biomagnified in the food webs of Rio de Janeiro bays.