peer reviewed ; This study investigates the occurrence of greenhouse gases (GHGs) and the role of groundwater as an indirect pathway of GHG emissions into surface waters in a gaining stretch of the Triffoy River agricultural catchment (Belgium). To this end, nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) concentrations, the stable isotopes of nitrate, and major ions were monitored in river and groundwater over 8 months. Results indicated that groundwater was strongly oversaturated in N2O and CO2 with respect to atmospheric equilibrium (50.1 vs. 0.55 μg L−1 for N2O and 14,569 vs. 400 ppm for CO2), but only marginally for CH4 (0.45 vs. 0.056 μg L−1), suggesting that groundwater can be a source of these GHGs to the atmosphere. Nitrification seemed to be the main process for the accumulation of N2O in groundwater. Oxic conditions prevailing in the aquifer were not prone for the accumulation of CH4. In fact, the emissions of CH4 from the river were one to two orders of magnitude higher than the inputs from groundwater, meaning that CH4 emissions from the river were due to CH4 in-situ production in riverbed or riparian zone sediments. For CO2 and N2O, average emissions from groundwater were 1.5 × 105 kg CO2 ha−1 year−1 and 207 kg N2O ha−1 year−1, respectively. Groundwater is probably an important source of N2O and CO2 in gaining streams but when the measures are scaled at catchment scale, these fluxes are probably relatively modest. Nevertheless, their quantification would better constrain nitrogen and carbon budgets in natural systems.