The transport, transformation and ultimate fate of phosphorus (P) in river systems are significantly influenced by hydrodynamic conditions. To investigate the effect of flow velocity on the P uptake by bed sediments, a series of laboratory experiments are carried out in an incubator shaker and an annular flume. The results showed a much longer equilibrium time and a slower rate of P uptake by bed sediments in the flume than those in batch experiments. The process of P uptake by bed sediments was divided into two stages: (i) in the first 24 h, the amount of P uptake increased with the increasing flow velocity and (ii) after 24 h, flow velocity had no significant effect on P uptake by bed sediments. The amount of P uptake appeared fluctuating over different velocities. The paper presents a linear relationship between the P fraction in the bed sediments and the square root of time lapsed, which indicates that the diffusional process of P from water column to bed sediments is the dominant process in controlling the P uptake by bed sediments. The slope and intercept of the regression line were controlled by the flow velocity. Of the two models used to describe the process of P uptake by bed sediments, the Elovich Equation appeared to be better than the boundary layer model due to its ability to distinguish the different uptake rates at different flow velocities.