Many species living in the hyporheic zone of rivers, such as fishes and benthos, are sensitive to the excessive presence of fine sediment. These particles tend to reduce the connectivity between the hyporheic zone and the surface flow by filling the pore and clogging the riverbed. The construction of dams, the regulation of the flow and straightening of rivers have increased the degree of clogging of many rivers in the past decades by changing the regime of floods and sediment transport. To propose solutions and improve the quality of river ecosystems, the knowledge on the process of clogging still needs to be improved. This study focuses on the influence of the exchanges between the groundwater and the surface flow on the clogging of the riverbed. This parameter, despite its importance, has been very little studied. In this research, the gradient of pressure between the surface flow and the groundwater has been systematically varied to observe its influence on permeability and the depth of clogging. Experiment were carried out in a flume and showed a much faster process of clogging for high gradient of infiltration. Fine sediment deposited in the substrate in all experiment including in the presence of upwelling. As fine sediment accumulate in the substrate, the filter resistance increase faster and does not present a linear increase as supposed in previous research.