The Patos Estuary, in southern Brazil, is subject to an irregular hydrological regime and receives mercury (Hg)-contaminated effluents from the city of Rio Grande since the colonial period of southern Brazil. Aiming to investigate sulfate reduction effects over Hg geochemistry in a shallow area (SA) and a salt marsh (SM) from the Patos Estuary, four sediment cores were collected during two distinct hydrological regimes (i.e., freshwater dominated and brackish water dominated). An assessment of free dissolved sulfide (ΣS−II) concentration and pH in pore water and metals (Fe and Hg), fine grained (<63μm) and organic carbon (OC) contents in sediment allowed us to conclude that mercury distribution in SA is chiefly controlled by <63μm sediments and metal sulfide formation. Furthermore, redox conditions were relatively stable during both sampling periods. Nevertheless, bioturbation promotes oxygen penetration and subsequent acidification of pore water associated with upper sediment layers in SM, especially during the brackish water period. Most likely, such oxidizing conditions hamper sulfate reduction and, thereafter, Hg immobilization via the formation of metal sulfides. No evidence of anthropogenic contamination was found in the studied sediments.