Identification of specific landscape areas with high and low groundwater denitrification potential is critical for improved management of agricultural nitrogen (N) export to ground and surface waters and indirect nitrous oxide (N2O) emissions. Denitrification products together with concurrent hydrogeochemical properties were analysed over two years at three depths at two low (L) and two high (H) permeability agricultural sites in Ireland. Mean N2O-N at H sites were significantly higher than L sites, and decreased with depth. Conversely, excess N2-N were significantly higher at L sites than H sites and did not vary with depth. Denitrification was a significant pathway of nitrate (NO3(-)-N) reduction at L sites but not at H sites, reducing 46-77% and 4-8% of delivered N with resulting mean NO3(-)-N concentrations of 1-4 and 12-15mgNL(-1) at L and H sites, respectively. Mean N2O-N emission factors (EF5g) were higher than the most recent Intergovernmental Panel on Climate Change (IPCC, 2006) default value and more similar to the older IPCC (1997) values. Recharge during winter increased N2O but decreased excess dinitrogen (excess N2-N) at both sites, probably due to increased dissolved oxygen (DO) coupled with low groundwater temperatures. Denitrifier functional genes were similar at all sites and depths. Data showed that highly favourable conditions prevailed for denitrification to occur - multiple electron donors, low redox potential (Eh<100mV), low DO (<2mgL(-1)), low permeability (ks<0.005m·d(-1)) and a shallow unsaturated zone (<2m). Quantification of excess N2-N in groundwater helps to close N balances at the local, regional and global scales.