Trophic relationships and trophic levels are important for understanding ecosystem structure and energy flow in food webs.Carbon and nitrogen stable isotope measurements have been used to assess trophic levels and sources of primary productivity in food webs.Mercury (Hg) is a micropollutant that can biomagnify in food chains, reaching high concentrations in top-chain organisms.Previous studies on stable isotope ratios and micropollutant flow have mainly focused on northern hemisphere areas, with limited research in tropical regions.The present study focuses on three tropical coastal ecosystems in Rio de Janeiro State: Guanabara, Sepetiba, and Ilha Grande bays.These bays have different levels of degradation, with Guanabara Bay being the most degraded and Ilha Grande Bay being the most preserved.The objectives of the study are to investigate trophic relationships, compare trophic structure, calculate trophic magnification factors of total mercury, and assess the influence of factors such as trophic position on mercury accumulation.