We are investigating nitrogen transformations and other biogeochemical processes associated with mixing of water masses within the near-shore aquifer and subterranean estuary of Waquoit Bay, Massachusetts. Where nitrate and ammonium co-occur in field settings, concentration and natural abundance N stable isotopic data suggest substantial loss of both species through a fractionating process. Laboratory experiments employing modified isotope pairing techniques confirm N loss with mixing of nitrate and ammonium-bearing waters and suggest that loss is primarily due to denitrification, possibly coupled to oxidation of Fe(II), with minor occurrence of an anammox-type process. Other concurrent processes included Mn reduction, substantial production or release of organic N, apparent ad/desorption of ammonium, and desorption or production of nitrate. Our results suggest that N is actively cycled in nearshore portions of coastal aquifers and that we need to consider a wide range of concurrent transformation pathways in submarine groundwater discharge zones. Such transformations have the potential to modify the composition of chemical loads carried by SGD. Further isotope pairing experiments are being conducted in flow-through sediment columns to simulate groundwater flow through coastal aquifer sediments.