We investigated biogeochemical conditions and watershed features controlling the extent of nitrate removal through microbial dinitrogen (N2) production within the surficial glacial aquifer located on the north and south shores of Long Island, NY, USA. The extent of N2 production differs within portions of the aquifer, with greatest N2 production observed at the south shore of Long Island where the vadose zone is thinnest, while limited N2 production occurred under the thick vadose zones on the north shore. In areas with a shallow water table and thin vadose zone, low oxygen concentrations and sufficient DOC concentrations are conducive to N2 production. Results support the hypothesis that in aquifers without a significant supply of sediment-bound reducing potential, vadose zone thickness exerts an important control of the extent of N2 production. Since quantification of excess N2 relies on knowledge of equilibrium N2 concentration at recharge, calculated based on temperature at recharge, we further identify several features, such as land use and cover, seasonality of recharge, and climate change that should be considered to refine estimation of recharge temperature, its deviation from mean annual air temperature, and resulting deviation from expected equilibrium gas concentrations.