Connectivity between the hyporheic zone and the flow is essential for the development of benthos and the reproductive success of spawning fish. The infiltration of fine sediment leads to clogging of the riverbed, reducing porosity and vertical water exchange. Natural clogging cycle is altered by infrastructure and land use. This chapter includes a short review of the process and influencing factors, which are illustrated with some experimental results. These principles are then applied to a selection of common cases.