Biogeochemically modified pore waters from subterranean estuaries, defined as the mixing zone between freshwater and saltwater in a coastal aquifer, are transported to coastal waters through submarine groundwater discharge (SGD). SGD has been shown to impact coastal and perhaps global trace metal budgets. The focus of this study was to investigate the biogeochemical processes that control arsenic cycling in subterranean estuaries. Total dissolved As, as well as a suite of other trace metals and nutrients, were measured in a series of wells and sediment cores at the head of Waquoit Bay, MA. Dissolved As ranged from below detection to 9.5 microg/kg, and was associated with plumes of dissolved Fe, Mn, and P in the groundwater. Sedimentary As, ranging from 360 to 7500 microg/kg, was highly correlated with sedimentary Fe, Mn, and P. In addition, amorphous Fe (hydr)oxides were more efficient scavengers of dissolved As than the more crystalline forms of solid-phase Fe. Given that dissolved As in the surface bay water was lower than within the subterranean estuary, our results indicate that the distribution and type of Fe and Mn (hydr)oxides in coastal aquifers exert a major influence on the biogeochemical cycling of As in subterranean estuaries and, ultimately, the fate of groundwater-derived As in marine systems influenced by SGD.