The reaction of phosphorus (P) between sediments and water in streams strongly affects the surface water P concentrations. A new reactive transport model (SWEMP: Sediment-Water Exchange Model for Phosphorus) was developed to describe redox dependent P sorption in the sediment and vertical diffusive transport of solutes to the overlying stream. The model parameters were independently obtained to first predict P release in ten different sediment-water batch systems and in two flumes. Input parameters are the degree of P saturation of the sediment, its organic matter content, dissolved oxygen (DO) concentration and temperature. The dissolved P concentrations in the overlying waters ranged from 0.02 to 1.2 mg P L−1 in these systems and were correctly predicted by the model within, on average, a factor 1.3 (batch) or 1.1 (flume). The P flux from the sediment towards the overlying water increased with increasing sediment P:Fe ratio and respiration rates, and with decreasing DO and water pH. After validation of the model with experimental data, it was used to predict monthly P concentrations in Flemish rivers using the total P emission data, total discharge, average sediment properties and the monthly averaged water temperatures, DO concentrations and electric conductivity. The monthly average P concentrations oscillate annually between 0.24 and 0.73 mg P L−1 and predictions matched the long-term monitoring data within 10 % using only one adjustable parameter for the entire water system (N > 250,000). The model predicts that summer peaks in P are related to internal loading from the sediment under anoxic conditions rather than to emission-dilution effects, i.e. external input of P and/or its concentration at lower flow rates. This suggests that, surface water P concentrations can be lowered by enhanced DO in the water, the addition of Fe and Al rich binding agents to the sediments and by reducing P emissions.