Pollutant exchange in the hyporheic zone is a major process controlling its degradation in river systems. Knowledge of mass transfer processes at the sediment-water interface (SWI) remains scarce. Accurate predictive modeling of flow driving pollutant fluxes at the SWI is currently limited. We examined mass exchange at the SWI by combining laboratory tracer experiments and the development of a flow reactive transport (FRT) model. NaCl and Foron Blue 291 tracers were used as surrogates of conservative and moderately sorptive organic pollutants, respectively. Tracer experiments in the bench-scale river channel reproduced the influence of overlying water velocities, the source of the pollutant, and its sorption capacity on pollutant exchange. A methodological framework to calibrate the FRT model against experiments was developed. Good agreement between the experimental and numerical results confirmed the robustness of the experimental setup and numerical model. The pollutant origin, either from the sediment or the overlying water, did not affect the pollutant exchange rates. The exchange rates were quasi-proportional to the overlying water velocity. The sediment bed caused retention of more than half of the initially injected mass of Foron Blue 291. The moderately sorptive tracer partitioning retarded the equilibrium up to six times compared with the conservative tracer NaCl. Numerical tests, including both overlying and vertical velocities, showed that the latter is the main factor controlling pollutant exchange at the SWI. Altogether, the model allows capturing interactions between pollutant transport and partitioning to the rivers sediment, paving the way for systematic investigations of pollutant behavior in rivers.