A gravity core (220 cm depth) was collected to investigate the geochemistry, enrichment, and pollution of trace metals in anoxic sediments from San Simon Bay, an ecosystem of high biological productivity in the northwest of Spain. A five-step sequential extraction procedure was used. The Cu, Pb, and Zn contents decreased with depth, with maximum values in the top layers. Ni and Zn were bound to pyrite fractions, while Cd and Pb were associated with the most mobile fractions. The analyzed metals were associated with the fractions bound to organic matter, mainly with the strongly bound to organic matter fraction. High Cd and Cu values were observed. The fractionation showed a high mobility for Cd (28.3–100%) and Pb (54.0–70.2%). Moreover, the pollution factor and the geoaccumulation index reflected a high contamination for Pb and a moderate contamination for Cu and Zn in the superficial layers, pointing to a possible ecotoxicological risk to organisms in San Simon Bay.