Mangrove ecosystems are essential to society, providing ecological and economic services, and play a crucial role in the geochemical land-ocean interface as a sink for potentially toxic metals. This study assessed metals (Al, Ba, Cd, Cr, Cu, Fe, Mn, Ni, Pb, Sr and Zn) and arsenic in sediments from three mangrove zones (Tidal Flat, Rhizophora mangle L. and Avicennia schaueriana Stapf & Leechman ex Moldenke forests) during two seasons: spring of 2015 and autumn of 2016, with the latter being a severe drought year. Overall results suggest that Fe/Mn oxyhydroxides and clay minerals control the distribution of metal and arsenic in the Tidal Flat zone. In the mangrove forest however, sulfur and organic matter dominate complexation, with Fe mainly present as insoluble sulfide, and As, Cd, Cu and Zn as metal sulfides or organometallic complexes. In the autumn of 2016, all elements except Cd and Pb had lower concentrations compared to the spring of 2015. Cd and Pb were probably transferred from sources other than mangrove sediments, due to increased saline water intrusion, a consequence of reduced riverine flow, and precipitated in the Rhizophora mangle and Avicennia schaueriana mangrove forests. This increase of Cd and Pb in the mangrove forest suggests potential storage of metal contaminants in the organic rich areas, a change in availability and potential toxicity to fauna and flora and a need for regulatory responses to sediment quality. These results indicate a change in sediment metal contaminant dynamics with the increasing occurrence of extreme weather events - an increased risk to the ecosystem.