Subterranean estuaries are characterized by the mixing of terrestrially derived groundwater and seawater in a coastal aquifer. Subterranean estuaries, like their river water-seawater counterparts on the surface of the earth, represent a major, but less visible, hydrological and geochemical interface between the continents and the ocean. This article is the first in a two-part series on the biogeochemistry of the subterranean estuary at the head of Waquoit Bay (Cape Cod, MA, USA). The pore-water distributions of salinity, Fe and Mn establish the salt and redox framework of this subterranean estuary. The biogeochemistry of Fe, Mn, P, Ba, U and Th will be addressed from the perspective of the sediment composition. A second article will focus on the groundwater and pore-water chemistries of Fe, Mn, U and Ba. Three sediment cores were collected from the head of Waquoit Bay where the coastal aquifer consists of permeable sandy sediment. A selective dissolution method was used to measure the concentrations of P, Ba, U and Th that are associated with “amorphous (hydr)oxides of iron and manganese” and “crystalline Fe and Mn (hydr)oxides.” The deeper sections of the cores are characterized by large amounts of iron (hydr)oxides that are precipitated onto organic C-poor quartz sand from high-salinity pore waters rich in dissolved ferrous iron. Unlike Fe (hydr)oxides, which increase with depth, the Mn (hydr)oxides display midcore maxima. This type of vertical stratification is consistent with redox-controlled diagenesis in which Mn (hydr)oxides are formed at shallower depths than iron (hydr)oxides. P and Th are enriched in the deep sections of the cores, consistent with their well-documented affinity for Fe (hydr)oxides. In contrast, the downcore distribution of Ba, especially in core 3, more closely tracks the concentration of Mn (hydr)oxides. Even though Mn (hydr)oxides are 200–300 times less abundant than Fe (hydr)oxides in the cores, Mn (hydr)oxides are known to have an affinity for Ba which is many orders of magnitude greater than iron (hydr)oxides. Hence, the downcore distribution of Ba in Fe (hydr)oxide rich sediments is most probably controlled by the presence of Mn (hydr)oxides. U is enriched in the upper zones of the cores, consistent with the formation of highly reducing near-surface sediments in the intertidal zone at the head of the Bay. Hence, the recirculation of seawater through this type of subterranean estuary, coupled with the abiotic and/or biotic reduction of soluble U(VI) to insoluble U(IV), leads to the sediments acting as a oceanic net sink of U. These results highlight the importance of permeable sediments as hosts to a wide range of biogeochemical reactions, which may be impacting geochemical budgets on scales ranging from coastal aquifers to the continental shelf.