Agricultural pollutants in catchments are transported toward the discharging stream through various flow routes such as tube drain flow, groundwater flow, interflow, and overland flow. Direct measurements of flow route contributions are difficult and often impossible. We developed a field-scale setup that can measure the contribution of the tube drain flow route to the total discharge toward the surface water system. We then embedded these field-scale measurements in a nested measurement setup to asses the value of field-scale measurements for interpretation of catchment-scale discharge and nitrate concentrations using a linear flow route mixing model. In a lowland catchment, we physically separated the tube drain effluent from the discharge of all other flow routes. Upscaling the field-scale flow route discharge contributions to the subcatchment and the catchment scale with a linear flow route mixing model gave a good prediction of the catchment discharge. Catchment-scale nitrate concentrations were simulated well for a heavy rainfall event but poorly for a small rainfall event. The nested measurement setup revealed that the fluxes at a single field site cannot be representative for the entire catchment at all times. However, the distinctly different hydrograph reaction of the individual flow routes on rainfall events at the field site made it possible to interpret the catchment-scale hydrograph and nitrate concentrations. This study showed that physical separation of flow route contributions at the field scale is feasible and essential for understanding catchment-scale discharge generation and solute transport processes.