Fine sediment represents an important part of the solid flux of rivers. Due to the size of these particles, they are often transported as suspended load. They gradually fill the pores of the substrate forming the hyporheic zone or cover the substrate by settling, resulting in the clogging of the riverbed. Clogging of the major part of the riverbed affects the habitat of invertebrates and reduces the reproduction success of spawning fish. This threat has been reported by a substantial amount of research in the past decades. Human infrastructure (such as reservoirs and hydropower plants), combined with artificial riverbanks and an increased flux of fine sediment in some catchments, has deeply changed the dynamic of rivers. A large number of studies have focused on the impact of clogging on aquatic fauna. The process of deposition of fine sediment has also been the subject of many studies aimed at understanding the role of different parameters (for example, the role of vertical distribution of fine sediment on substrate clogging). Here, the physical mechanisms involved in the deposition of fine sediment are reviewed to give a more comprehensive overview of this complex process. A general description of the process is followed by an analysis of the different parameters that are involved. The influence of flow conditions, substrate composition, hyporheic flow and fine sediment characteristics are analysed in detail. The different models that have been proposed to estimate the depth, quantity and time evolution of the process are also presented. Declogging - the release of fine sediment into the surface flow - is also described according to the existing literature on the subject of fine sediment transport. The clogging process is then reviewed at a larger scale with field aspects that include spatial and temporal parameters linked to flood events, sediment transport, hydropeaking and flushing of reservoirs. Finally, a synthesis of the clogging process is performed together with a dimensional analysis of key elements, followed by a discussion on the research gaps.