Multi-element analyses of sediment samples from the Santos-Cubatão Estuarine System were carried out to investigate the spatial and seasonal variability of trace-element concentrations. The study area contains a rich mangrove ecosystem that is a habitat for tens of thousands of resident and migratory birds, some of them endangered globally. Enrichments of metals in fine-grained surface sediments are, in decreasing order, Hg, Mn, La, Ca, Sr, Cd, Zn, Pb, Ba, Cu, Cr, Fe, Nb, Y, Ni and Ga, relative to pre-industrial background levels. The maximum enrichment ranged from 49 (Hg) to 3.1 (Ga). Mercury concentrations were greater in the Cubatão river than in other sites, while the other elements showed greater concentrations in the Morrão river. Concentrations of Mn were significantly greater in winter and autumn than in summer and spring. However, other elements (e.g. Cd and Pb) showed the opposite, with greater concentrations in summer and spring. This study suggests that seasonal changes in physical and chemical conditions may affect the degree of sediment enrichment and therefore make the assessment of contamination difficult. Consequently, these processes need to be considered when assessing water quality and the potential contamination of biota.