Freely discharging lowland catchments are characterized by a strongly seasonal contracting and expanding system of discharging streams and ditches. Due to this rapidly changing active channel network, discharge and solute transport cannot be modeled by a single characteristic travel path, travel time distribution, unit hydrograph, or linear reservoir. We propose a systematic spatial averaging approach to derive catchment-scale storage and discharge from point-scale water balances. The effects of spatial heterogeneity in soil properties, vegetation, and drainage network are lumped and described by a relation between groundwater storage and the spatial probability distribution of groundwater depths with measurable parameters. The model describes how, in lowland catchments, the catchment-scale flux from groundwater to surface water via various flow routes is affected by a changing active channel network, the unsaturated zone and surface ponding. We used observations of groundwater levels and catchment discharge of a 6.6 km2 Dutch watershed in combination with a high-resolution spatially distributed hydrological model to test the model approach. Good results were obtained when modeling hourly discharges for a period of eight years. The validity of the underlying assumptions still needs to be tested under different conditions and for catchments of various sizes. Nevertheless, at this stage the model can already improve monitoring efficiency of groundwater-surface water interactions.