Coastal sedimentary systems are affected by continental and marine metal pollutant inputs associated with different hydrodynamic characteristics and geochemical processes. These include the formation of acid-volatile sulfides (AVS) within sediments, which affects metal bioavailability and associated aquatic biota toxicity risks. Physicochemical changes in these environments in the face of extreme natural or man-made environmental influences can dramatically alter metal bioavailability and toxicity through metal binding and immobilization as insoluble sulfides. Surface sediments from Guanabara Bay, river mouths, and two mangrove areas were collected, and AVS and simultaneously extracted metals Cd, Cu, Fe, Mn, Ni, Pb, and Zn and ΣSEM were determined to assess sediment quality. A severe eutrophication history favored AVS concentrations exceeding or close to the sum-SEM concentrations, demonstrating that AVS play an important role in making trace metals unavailable for assimilation by living organisms, mitigating the risks of contamination for the local biota. This eutrophication-driven sulfide accumulation may attenuate the sediment toxicity in sites heavily polluted by metals, while some fewer eutrophic sites became more exposed to metals in excess to AVS.