Groundwater is an important pathway for terrestrially derived nutrients to enter the coastal ocean. In coastal aquifers, groundwater transits the subterranean estuary, a region of sharp gradients in redox conditions and the availability of reactants. In one such system (Waquoit Bay, MA, USA), we observed more than a doubling of the groundwater-associated nitrogen flux to surface water during the summer compared to winter due primarily to a reduction in nitrogen attenuation within the subterranean estuary. Because marine groundwater intrusion has been shown to increase during the summer, we calculate a greater contribution of recycled nutrients from the coastal ocean to the subterranean estuary. We posit that the longer residence times within the subterranean estuary during the winter, which would result from reduced marine groundwater circulation, allow oxygen depletion of the groundwater, creating a favorable environment for important nutrient transformations such as nitrification, denitrification, and anammox. The timing of nutrient delivery to the coastal ocean has important implications for coastal marine ecology including the potential development of harmful algal blooms.