Riverbed sediments have recently been found to be an important reservoir for microplastics. But the hydrogeological factors that control the abundance of microplastics are complex and conceptual frameworks priorising the parameters affecting their transport and retention during deep riverbed filtration are still missing. In this study a series of saturated column experiments was conducted to investigate the vertical distribution patterns of secondary polystyrene fragments (100–2000 μm) in dependence on their particle size, grain size of the sediment, seepage velocity and duration of infiltration flow. The columns with a length of 50 cm were operated with flow velocities between 1.8 m d−1 and 27 m d−1. Invasive samples obtained after the experiments were density separated and then depth profiles of microplastic concentrations were retrieved using fluorescence imaging analysis. Most polystyrene particles were retained in the upper 20 cm and 15 cm of the medium gravel and coarse sand sediments, respectively. Through the high particle retention riverbed sediments can act as a temporary sink or long term retention site for the transport of microplastic particles (MPPs) from streams to oceans. A small fraction of particles ranging from 100 to 500 μm in size was observed down to infiltration depths of 50 cm suggesting that MPPs at the pore scale have the potential to be advectively transferred via hyporheic exchange or induced bank filtration into coarse riverbed sediments and alluvial aquifers. MPP abundance over column depth follows an exponential relationship with a filter coefficient that was found to depend significantly on the flow rate, MPP and sediment grain size, as indicated by multiple linear regression (R2 = 0.92). The experimentally derived empirical relation allows to estimate particle abundances of initially negatively buoyant MPP in riverbed sediments by surface water infiltration.