We constructed a survey system of radon/methane/nitrate/salinity to find sites of submarine groundwater discharge (SGD) and groundwater nitrate input. We deployed the system in Waquoit Bay and Boston Harbor, MA where we derived SGD rates using a mass balance of radon with methane serving as a fine resolution qualitative indicator of groundwater. In Waquoit Bay we identified several locations of enhanced groundwater discharge, out of which two (Childs and Quashnet Rivers) were studied in more detail. The Childs River was characterized by high nitrate input via groundwater discharge, while the Quashnet River SGD was notable but not a significant source of nitrate. Our radon survey of Boston Harbor revealed several sites with significant SGD, out of these Inner Harbor and parts of Dorchester Bay and Quincy Bay had groundwater fluxes accompanied by significant water column nitrogen concentrations. The survey system has proven effective in revealing areas of SGD and non-point source pollution.