The concentrations of both major and trace elements in San Simón Bay's subtidal sediments were determined for the purposes of (1) evaluating the influence of anthropogenic activities on metal content (against pre-anthropogenic background values attained via the deepest core samples), (2) establishing the subtidal sediments' degrees of pollution in recent decades, and (3) determining the influence of mussel raft systems on the composition of bottom sediments. Subtidal sediments consist of laminated, organic-rich, fine-grained sediments with low carbonate content and a notable presence of gas in their lower part. The recent sedimentary record revealed pollution, mainly from Pb and Cu, rising toward the sediment surface. The sources of various heavy metals were accordingly identified, with the application of Principal Component Analysis to discriminate among the different metal sources. It has been found that the mineralogy of the catchment area determines the overall composition, whereas biogenic production and anthropogenic activities contribute to the total metal content. At the same time, mariculture influences the composition of underlying sea bottom sediments, by changing the inorganic carbon content. Finally, evidence is provided to show how sediment composition is tied mainly to aquaculture and watershed characteristics via conditioning by anthropogenic activities.