Pharmaceutical residues are commonly detected micropollutants in the aquatic environment. Biodegradation in sediments is a potentially significant removal process for these compounds in rivers which is constrained by the transfer of water and solutes into the sediment. The aim of this study was to determine the combined effect of flow velocity and sediment dynamics and thus of water-sediment interactions on the attenuation of 6 acidic pharmaceuticals. We carried out experiments with river water and sediment in a bench-scale annular flume at two different hydraulic boundary conditions (flat sediment surface vs moving sediment). The effective biodegradation half-lives of 4 compounds (diclofenac, bezafibrate, ibuprofen, naproxen) were in the range of 2.5 to 18.6 days and were much shorter when the exchange of surface and pore water was fast. For gemfibrozil, a half-life of 10.5 d was determined in the experiment with moving sediment, whereas no degradation was observed with flat sediment bed. These findings can be attributed to the limited transfer of water and solutes into the sediment at low flow velocity and flat sediment bed which rapidly induced anaerobic conditions in the sediment. The only compound that was efficiently removed in deeper, anoxic sediment layers was naproxen. The calculated half-life distances in rivers ranged from 53 to 278 km. Our results indicate that it could be favorable to increase the rate of exchange between surface and pore water during river restoration to enhance the attenuation of organic micropollutants like acidic pharmaceuticals.