N2O flux from aquifers caused by leaching of agricultural N is a poorly known component of the global anthropogenic source of this greenhouse gas. We measured isotopomer signatures of N2O (intramolecular distribution of 15N as well as conventional nitrogen and oxygen isotope ratios) in the interface region between shallow groundwater and the atmosphere in order to evaluate this technique for determining fluxes, production, reduction and the isotopomer fingerprint of N2O originating from the saturated zone. 15N-site preference (difference in δ15N between central and peripheral N-position) measured in the shallow groundwater of a hydromorphic soil (29 to 81?) was distinctly larger compared to surface emitted N2O. Local and global isotopic budget calculations confirmed that the groundwater derived N2O flux of the experimental site was low compared to measured surface fluxes and suggest that 15N-site preference might be useful for validating global estimates of groundwater emitted N2O.