Estimating losses of dissolved carbon (C) and nitrogen (N) via groundwater in an agricultural system provides insights into the reduction of uncertainties in the terrestrial C and N balances. In addition, quantification of dissolved nitrous oxide (N₂O), carbon dioxide (CO₂) and methane (CH₄) in groundwater beneath an agricultural system is of huge importance for global greenhouse gas (GHG) budget estimation. Dissolved C (DC: dissolved organic carbon (DOC)+CO₂+CH₄) and dissolved nitrogen (DN: NO₃^--N+NH₄⁺+NO₂^-+N₂O+N₂) in groundwater were measured in two low permeability (<0.02 m d^-1) and two high permeability (>0.05 m d^-1) aquifers in Ireland. Groundwater in multilevel piezometers was sampled monthly over two years (Feb, 2009 to Jan, 2010). Mean groundwater discharge to surface water was higher in 2009 (587-836 mm) than that 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. Mean N₂O emissions via groundwater ranged from 201- 276 kg of CO₂ equivalence ha^-1 y^-1. The N₂O emissions 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 was not significant compared to total carbon (TC) content of the topsoil (0.06-0.18% of TC). However, CO₂ emissions was an important source of atmospheric CO₂ (mean 537-1041 kg ha^-1 y^-1). Methane emissions via groundwater were 1 to 30 kg of CO₂ equivalence ha^-1 y^-1. Indirect GHG from groundwater were an important part of farm budgets, which clearly has implications for national inventories.