Submarine groundwater discharge (SGD) is an important source of dissolved elements to the ocean, yet little is known regarding the chemical reactions that control their flux from sandy coastal aquifers. The net flux of elements from SGD to the coastal ocean is dependent on biogeochemical reactions in the groundwater-seawater mixing zone, recently termed the "subterranean estuary". This paper is the second in a two part series on the biogeochemistry of the Waquoit Bay coastal aquifer/subterranean estuary. The first paper addressed the biogeochemistry of Fe, Mn, P, Ba, U, and Th from the perspective of the sediment composition of cores (Charette et al., 2005). This paper uses pore water data from the subterranean estuary, along with Bay surface water data, to establish a more detailed view into the estuarine chemistry and the chemical diagenesis of Fe, Mn, U, Ba and Sr in coastal aquifers.Nine high-resolution pore water (groundwater) profiles were collected from the head of the bay during July 2002. There were non-conservative additions of both Ba and Sr in the salinity transition zone of the subterranean estuary. However, the extent of Sr release was significantly less than that of its alkaline earth neighbor Ba. Pore water Ba concentrations approached 3000 nM compared with 25-50 nM in the surface waters of the bay; the pore water Sr-salinity distribution suggests a 26 % elevation in the amount of Sr added to the subterranean estuary. The release of dissolved Ba to the mixing zone of surface estuaries is frequently attributed to an ion-exchange process whereby seawater cations react with Ba from river suspended clay mineral particles at low to intermediate salinity. Results presented here suggest that reductive dissolution of Mn oxides, in conjunction with changes in salinity, may also be an important process in maintaining high concentrations of Ba in the pore water of subterranean estuaries.In contrast, pore water U was significantly depleted in the subterranean estuary, a result of SGD-driven circulation of seawater through reducing permeable sediments. This finding is supported by surface water concentrations of U in the bay, which were significantly depleted in U compared with adjacent coastal waters. Using a global estimate of SGD, we calculate U removal in subterranean estuaries at 20 x 10 6 mol U y -1 , which is the same order of magnitude as the other major U sinks for the ocean. Our results suggest a need to revisit and reevaluate the oceanic budgets for elements that are likely influenced by SGD-associated processes.3