Stable isotopes of oxygen, nitrogen, and boron were used to identify the sources of nitrate (NO 3 −) in submarine groundwater discharge (SGD) into a large tidal estuary (Long Island Sound, NY, United States). Potential contaminants such as manure, septic waste and fertilizer overlap in δ 15 N and δ 18 O but have been shown to have distinctive δ 11 B in non-coastal settings. Two distinct subterranean estuaries were studied with different land-use up gradient, representative of (1) mixed medium-density residential housing and (2) agriculture. These sites have overlapping δ 15 N and δ 18 O measurements in NO 3 − and are unable to discriminate between different N sources. Boron isotopes and concentrations are measurably different between the two sites, with little overlap. The subterranean estuary impacted by mixed medium-density residential housing shows little correlation between δ 11 B and [B] or between δ 11 B and salinity, demonstrating that direct mixing relationships between fresh groundwater and seawater were unlikely to account for the variability. No two sources could adequately characterize the δ 11 B of this subterranean estuary. Groundwater N at this location should be derived from individual homeowner cesspools, although measured septic waste has much lower δ 11 B compared to the coastal groundwaters. This observation, with no trend in δ 11 B with [B] indicates multiple sources supply B to the coastal groundwaters. The agricultural subterranean estuary displayed a positive correlation between δ 11 B and [B] without any relationship with salinity. Binary mixing between sea spray and fertilizer can reasonably explain the distribution of B in the agricultural subterranean estuary. Results from this study demonstrate that δ 11 B can be used in combination with δ 15 N to trace sources of NO 3 − to the subterranean estuary if source endmember isotopic signatures are wellconstrained, and if the influence of seawater on δ 11 B signatures can be minimized or easily quantified.