This chapter reports a thorough study of the geochemistry of some metals in the sediments of the Patos lagoon, one of the biggest coastal lagoons in the world (and the biggest in Brazil). After a screening study of the sediments, which considered the granulometry, organic carbon, organic nitrogen and sulphur contents, Pb, Cu, Zn and Cr concentrations of more than 100 samples collected all over the system, the relationships between these variables were considered in order to explain their distribution. The distribution of metals within different granulometric fractions was also studied. Finally a sequential extraction procedure was performed in selected samples to provide information on the geochemical partitioning of the metals in the sediments. The absence of direct anthropogenic sources of metals to the lagoon was established. The main source of metals is the Guaiba system (northern portion), whose material is spread all over the lagoon and can be concentrated in the areas where physico-chemical parameters are favourable. The Camaquã river also constitutes a significant source of Cu and Pb for the southern portion of the Patos Lagoon, originating from the mining of metallic sulphides.