Dissolved and particulate metals (Ag, Cd, Co, Cu, Ni, and Zn) and nutrients (PO4, NO3, and H4SiO4) were measured in Todos Santos Bay (TSB) in August 2005. Two sources producing local gradients were identified: one from a dredge discharge area (DDA) and another south of the port and a creek. The average concentrations of dissolved Cd and Zn (1.3 and 15.6 nM, respectively) were higher by one order of magnitude than the surrounding Pacific waters, even during upwelling, and it is attributed to the presence of a widespread and long-lasting red tide coupled with some degree of local pollution. A clear spatial gradient (10 to 6 pM), from coast to offshore, of dissolved Ag was evident, indicating the influence of anthropogenic inputs. The particulate fraction of all metals, except Cu, showed a factor of ~3 decrease in concentrations from the DDA to the interior of the bay. The metal distributions were related to the bay’s circulation by means of a numerical model that shows a basically surface-wind-driven offshore current with subsurface compensation currents toward the coast. Additionally, the model shows strong vertical currents over the DDA. Principal component analysis revealed three possible processes that could be influencing the metal concentrations within TSB: anthropogenic inputs (Cd, Ag, and Co), biological proceses (NO3, Zn, and Cu), and upwelling and mixing (PO4, H4SiO4, Cd, and Ni). The most striking finding of this study was the extremely high Cd concentrations, which have been only reported in highly contaminated areas. As there was a strong red tide, it is hypothesized that the dinoflagellates are assimilating the Cd, which is rapidly remineralized and being concentrated on the stratified surface layers.