Hyporheic exchange is an ecologically important process, controlling the nutrient supply in the upper sediments and thus benthic habitat quality. Hydraulic exchange at a riffle-pool sequence in the Lahn River, Germany, was analyzed using HEC-RAS to simulate the surface water flow as a boundary for the subsurface flow and MODFLOW, MODPATH, and MT3DMS to reproduce the transport in the subsurface. Solute transport and residence times of surface water in the subsurface were simulated after calibrating sediment properties to fit simulated hydraulic head to measured subsurface head from the riffle-pool pair. Three surface water flow rates were considered. Results indicated that exchange increases with increasing surface water flow. However, the hydraulic conductivity of the riverbed sediments influences the mass transfer more than the surface water flow. The ratio of the infiltration rate to the surface water flow is of the same order of magnitude for all the considered flow conditions. Residence times of surface water in the subsurface varied inversely with the flow rates in the river.