Excess fine sediment, comprising particles <2 mm in diameter, is a major cause of ecological degradation in rivers. The erosion of fine sediment from terrestrial or aquatic sources, its delivery to the river, and its storage and transport in the fluvial environment are controlled by a complex interplay of physical, biological and anthropogenic factors. Whilst the physical controls exerted on fine sediment dynamics are relatively well-documented, the role of biological processes and their interactions with hydraulic and physico-chemical phenomena has been largely overlooked. The activities of biota, from primary producers to predators, exert strong controls on fine sediment deposition, infiltration and resuspension. For example, extracellular polymeric substances (EPS) associated with biofilms increase deposition and decrease resuspension. In lower energy rivers, aquatic macrophyte growth and senescence are intimately linked to sediment retention and loss, whereas riparian trees are dominant ecosystem engineers in high energy systems. Fish and invertebrates also have profound effects on fine sediment dynamics through activities that drive both particle deposition and erosion depending on species composition and abiotic conditions. The functional traits of species present will determine not only these biotic effects but also the responses of river ecosystems to excess fine sediment. We discuss which traits are involved and put them into context with spatial processes that occur throughout the river network. Whilst strides towards better understanding of the impacts of excess fine sediment have been made, further progress to identify the most effective management approaches is urgently required through close communication between authorities and scientists.