Fine particles are necessary for watershed biogeochemical cycling and stream metabolic processes but pose a risk to water quality if present in excess or if carrying sorbed contaminants. Despite having low settling velocities, these particles can leave suspension during downstream transport by a series of processes such as hyporheic filtration, flocculation, and biofilm entrapment. The objective of this study is to evaluate the retention of clay particles within a stream reach due to streambed filtration. To this end, we quantify hyporheic exchange through coupled formulations of turbulent surface water flow in the overlying stream and saturated groundwater flow in the streambed. Particle filtration models are informed by flow-through column experiments conducted with repacked streambed material. Results of our model simulations of hyporheic exchange demonstrate that streambed particle filtration depends on overlying streamflow and, to a lesser extent, on hyporheic zone substrate. Retention of suspended particles within the streambed sediments more than doubles between high and drought flows and varies by less than 45% across substrate grain size classes.