The impact of diffuse pollution, agricultural land use and climate change on the long-term response of subsurface–surface water quality is not well understood, but is a prerequisite for evaluation of water management options. The goal of this study is to model geochemical evolution of water chemistry from the infiltration through soil into the unsaturated zone, transport through bedrocks and granular aquifers to a river in order to identify zones of steep concentration gradients and high dynamics under transient flow conditions. A numerical model was constructed comprising a 2-D 1,500 m × 150 m vertical cross-section of typical sedimentary rock formations, a glacio-fluvial quaternary gravel aquifer in the valley and soil layers. The model coupled saturated/un-saturated flow and reactive transport under steady state and transient conditions. Geochemical interactions, include intra-aqueous kinetic reactions of oxygen with dissolved organic matter, as well as kinetics of carbonate dissolution/precipitation. This model section was chosen to provide insight in to the principal processes and time scales affecting water chemistry along different flow paths. The numerical simulator MIN3P was used, a finite volume program for variably saturated subsurface flow and multi-component reactive transport. The results show that subsurface water residence times range from approximately 2 to 2,000 years. Different zones are to be expected with respect to the development of mineral equilibria; namely, purely atmospherically influenced, as well as open and closed system carbonate dissolution. Short-term responses to daily averaged changes in precipitation, however, are only visible to some extent in the shallower and near-river parts of flow system and solute loads. This can most likely be explained by directional changes in flow paths, indicating that equilibrium geochemical condition predominate at the hillslope scale, i.e. water quality depends on transport pathways rather than on kinetic effects. The extent of reducing conditions is controlled by the presence of organic-rich layers (i.e. peat deposits), the dissolution kinetics of aquifer organic matter and the subsequent mixing with oxygenated water by hydrodynamic dispersion.