Iron and sulfur are key elements in the biogeochemistry of estuarine soils, in which Fe and sulfate reduction (SR) pathways are important for organic matter decomposition. In the semi-arid coast of NE Brazil, mangroves are characterized by large seasonal variations in weather and the presence of numerous shrimp farms. The objective was to determine the impacts of shrimp farm effluents on iron and sulfur geochemistry in mangrove soils under the semi-arid climate of NE Brazil. A seasonal study was made of two mangrove forest soils (SF, a mangrove forest that directly receives wastewater from shrimp ponds and CS, a control site). Pyrite Fe, oxyhydroxides Fe, acid volatile sulfide, degree of pyritization (DOP), pH, Eh, total organic carbon (TOC) and total S were determined. There was a clear decrease in pyritic Fe and DOP in the SF soils, which may be related to the anaerobic oxidation of pyrite coupled with nitrate reduction, or to the dominance of denitrification over SR. Lower TOC contents in the SF site suggest that below ground decomposition increased in response to eutrophication. The seasonal variations led to important changes in the semi-arid mangrove soils. During the dry period, both soils experienced oxidizing conditions with remarkable loss of reduced and oxidized forms of Fe, which may have important environmental implications as Fe is biolimiting for marine primary production. The data show that both factors (seasonal weather variations and shrimp effluents) play important roles in the geochemical processes that occur in these soils and, thus, may affect their functioning and maintenance.