We report a data-set of CO2, CH4, and N2O concentrations in the surface waters of the Meuse river network in Belgium, obtained during four surveys covering 50 stations (summer 2013 and late winter 2013, 2014 and 2015), from yearly cycles in four rivers of variable size and catchment land cover, and from 111 groundwater samples. Surface waters of the Meuse river network were over-saturated in CO2, CH4, N2O with respect to atmospheric equilibrium, acting as sources of these greenhouse gases to the atmosphere, although the dissolved gases also showed marked seasonal and spatial variations. Seasonal variations were related to changes in freshwater discharge following the hydrological cycle, with highest concentrations of CO2, CH4, N2O during low water owing to a longer water residence time and lower currents (i.e. lower gas transfer velocities), both contributing to the accumulation of gases in the water column, combined with higher temperatures favourable to microbial processes. Inter-annual differences of discharge also led to differences in CH4 and N2O that were higher in years with prolonged low water periods. Spatial variations were mostly due to differences in land cover over the catchments, with systems dominated by agriculture (croplands and pastures) having higher CO2, CH4, N2O levels than forested systems. This seemed to be related to higher levels of dissolved and particulate organic matter, as well as dissolved inorganic nitrogen in agriculture dominated systems compared to forested ones. Groundwater had very low CH4 concentrations in the shallow and unconfined aquifers (mostly fractured limestones) of the Meuse basin, hence, should not contribute significantly to the high CH4 levels in surface riverine waters. Owing to high dissolved concentrations, groundwater could potentially transfer important quantities of CO2 and N2O to surface waters of the Meuse basin, although this hypothesis remains to be tested.