Estimating losses of dissolved carbon (C) and nitrogen (N) via groundwater in an agricultural system provides insights into reducing uncertainties in the terrestrial C and N balances. In addition, quantification of dissolved nitrous oxide (N2O), carbon dioxide (CO2) and methane (CH4) in groundwaters beneath agricultural systems is important for global greenhouse gas (GHG) budgets. Dissolved C (DC: dissolved organic carbon (DOC) + CO2-C + CH4-C) and dissolved nitrogen (DN: NO3−-N + NH4+ + NO2−-N + N2O-N + N2) in groundwater were measured in two low permeability (0.05 m d−1) aquifers in Ireland. Groundwater in multilevel piezometers was sampled monthly over two years. Mean groundwater discharge to surface water was higher in 2009 (587–836 mm) than in 2010 (326–385 mm). Dissolved C and N delivery to surface water via groundwater caused substantial losses of terrestrial C and N. The extent of delivery was site specific and depended on N input, recharge and aquifer permeability. Mean dissolved N losses ranged from 8–12% of N input in low permeability to 27–38% in high permeability aquifers. The dominant fraction of DN was NO3−-N (84–90% of DN) in high permeability aquifers and N2 (46–77% of DN) in low permeability aquifers. Indirect N2O emissions via groundwater denitrification accounted for 0.03–0.12% of N input, which was equivalent to 3–11% of total N2O emissions. Dissolved C loss to surface waters via groundwater was not significant compared to total carbon (TC) content of the topsoil (0.06–0.18% of TC). Site characteristics contributed greatly to the distribution of N between NO3−-N and dissolved N gases, N2O and N2. Indirect GHG emissions from groundwater were an important part of farm nutrient budgets, which clearly has implications for national GHG inventories. ; peer-reviewed ; Department of Agriculture, Food and the Marine, Ireland - Research Stimulus Fund Programme (Grant RSF 06383); Department of Civil, Structural and Environmental Engineering, Trinity College Dublin