The mobilization and mixing of sediments by the activities of streambed inhabitants, referred to as sediment reworking, constantly modify the physical and hydraulic properties of streambeds. However, limited progress has been made to explore the influence of this sediment-organism interaction on hyporheic exchange. In this work, we advance the understanding of the role of macroinvertebrate sediment reworking in altering the hyporheic exchange flows in clogged streambeds. Laboratory experiments are conducted in re-circulating flumes following a control (clogging) and treatment (clogging + sediment reworking) based design. The experiments involve studying the interaction of model organisms (Lumbriculus variegatus) with fine sediment (clay) deposits, and its subsequent influence on hyporheic flow regime in homogenous model streambeds comprising fine sand, coarse sand, and gravel sediments. We observe that model organisms burrowed extensively into the clogging layer, mixed the clay particles with underlying grains, and eventually eroded or disintegrated the clogging layer at the bed surface in the treatment flumes. As a consequence, the treatment flumes exhibited greater solute penetration depth, shorter median and mean residence times, and higher hyporheic flux compared to their respective control flumes. The results also suggest that the modification of hyporheic exchange flows depends on the overall reworking of the beds including both fine and substrate sediments. The alteration of hydro-physical properties of streambeds and subsequently the hyporheic flow regime due to sediment reworking has direct implications for the biogeochemistry of hyporheic zones and may impact the overall quality of surface and sub-surface waters, particularly in low flow environments.