Riverbed sediments are the interface layer in riverine ecosystems connecting the overlying medium of water and the vadose zone. The transport behavior of phosphorus (P), which has been recognized as the primary cause of freshwater eutrophication, in riverbed sediments remains unclear. Understanding the impact of riverbed sediments on P transport is a necessary prerequisite for the development of appropriate strategies to reduce potential groundwater pollution. In this study, riverbed sediments were collected from the upstream, midstream, and downstream sections of the Beiyun River, China, and packed into vertical soil columns to perform leaching experiments to quantify P transport characteristics. In addition, the impact mechanisms were further explored by conducting laboratory batch tests of P adsorption and desorption. The results demonstrated that approximately 80% of P can be adsorbed by riverbed sediments in soil column leaching experiment, and a tailing phenomenon was observed in its desorption. The hydraulic conductivity properties of riverbed sediments were evaluated by the advection-dispersion equation, showing a gradually decreasing adsorption capacity for P from upstream to downstream sections, which was supported by the results obtained from adsorption–desorption thermodynamic and kinetic batch tests. The estimated annual leaching masses of P increased from 60.72 g/(m² a) in the upstream section to 132.31 g/(m² a) in the downstream section. The role of riverbed sediments as a source or sink of P is possibly determined by their coarse sand particles content, and the mean equilibrium P concentration (EPC0). The competitive relationship between P and other forms of nutrients also has an important influence on its source-sink role. These findings suggest that the prevention of the potential P leaching is most needed in the downstream sections of Beiyun River, and corresponding control strategies should be developed to avoid groundwater pollution.