Nitrate pollution of surface waters is widespread in lowland catchments with intensive agriculture. For identification of effective nitrate concentration reducing measures the nitrate fluxes within catchments need to be quantified. In this paper we applied a mass transfer function approach to simulate catchment-scale nitrate transport. This approach was extended with time-varying travel time distributions and removal of nitrate along flow paths by denitrification to be applicable for lowland catchments. Numerical particle tracking simulations revealed that transient travel time distributions are highly irregular and rapidly changing, reflecting the dynamics of rainfall and evapotranspiration. The solute transport model was able to describe 26 years of frequently measured chloride and nitrate concentrations in the Hupsel Brook catchment (6.6 km2 lowland catchment in the Netherlands) with an R2 value of 0.86. Most of the seasonal and daily variations in concentrations could be attributed to temporal changes of the travel time distributions. A full sensitivity analysis revealed that measurements other than just surface water nitrate and chloride concentrations are needed to constrain the uncertainty in denitrification, plant uptake, and mineralization of organic matter. Despite this large uncertainty, our results revealed that denitrification removes more nitrate from the Hupsel Brook catchment than stream discharge. This study demonstrates that a catchment-scale lumped approach to model chloride and nitrate transport processes suffices to accurately capture the dynamics of catchment-scale surface water concentration as long as the model includes detailed transient travel time distributions.