Only in the years 2007-2016 about 8000 large dams were constructed all over the world, adding to >50,000 previously built dams. These structures disturb abiotic and biotic components of rivers, but to date the knowledge of their impacts has been mainly derived from observations of downstream river reaches. Upstream from dams, however, backwater fluctuations induce sediment deposition, cause more frequent and higher valley-floor inundation, increase groundwater level, and change channel morphology and riparian vegetation. Little is known on the effects of these disturbances on the river biogeomorphological processes. In this review I synthesized knowledge on backwater effects on rivers into a model of backwater-induced abiotic-biotic interactions in the fluvial system. This model is next used to propose new hypotheses and research tasks concerning the biogeomorphology of gravel-bed rivers in the temperate climatic zone. Implications for flow-sediment-morphology-vegetation interactions and feedbacks are conceptualized in a river cross-section based on recent biogeomorphological insights and methodological approaches allowing to explore them in future studies. The model highlights that backwater-induced changes in abiotic and biotic components of river system trigger further feedbacks between them that additionally influence these components even without a direct backwater influence. Backwater-induced changes in hydrodynamics and sediment transport favour seed germination and growth of plants and decrease their mortality during floods, but also eliminate plants intolerant to prolonged inundation and intensive fine sediment deposition. These impacts may change the biogeomorphical structure of river system by modifying trajectories of biogeomorphic succession cycles and related zones of vegetation-hydromorphology interactions in the river corridor. Specifically, backwater effects may promote the development of more stable channel morphology and a less diverse mosaic of riparian vegetation and animals habitats, contrasting with those occurring in free-flowing rivers of the temperate zone.