Bioavailability assessment is important for evaluating the risks to the local biota, and the combined use of several ecological risk indices in eutrophic environments allows the best analysis of the local reality for decision-making. The relationship between acid volatile sulfide (AVS) concentrations and simultaneously extracted metals (SEM) allows us to infer the metal holding capacity of sediment, with the objective of evaluating the potential bioavailability of trace metals (Cd, Cu, Ni, Pb, and Zn) using ecological risk indices, such as the ΣSEM/AVS model and Adverse Effect Index (AEI), in surface sediments from Guanabara Bay and Sepetiba Bay, Brazil. AVS was determined using a colorimetric method and SEM with ICP-OES. In general, almost all sampling in Sepetiba Bay showed ΣSEM/AVS ratio values above 1. However, all results for the ΣSEM/AVS ratio found for the Guanabara Bay sediments were <1 for both estuaries. After normalization by organic carbon content, a possible toxicity risk for biota was found in Sepetiba Bay. However, the AEI in Guanabara Bay was above 1 for all metals in most samples, also indicating a risk to the biota.