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River ecosystem is spatiotemporally dynamic under frequent and intensive geomorphic disturbances, characterized by its fluctuating habitat availability. The species inhabiting there adapt themselves to the shifting habitat by developing various life-history strategies. In regulated rivers, however, suppressed disturbance and habitat dynamics threaten the disturbance-dependent communities. The recognition of important geomorphic perspectives is still in its infancy in conservation of river ecosystems in Japan. Riparian tree species have developed life-history strategies to increase the likelihood of arriving regeneration sites, where disturbance regimes are closely linked to the spatial and temporal availability of regeneration sites. River damming and channel modification severely diminish the critical function of geomorphic disturbance sustaining habitat diversity and abundance. Channel migration ceases in flow-regulated rivers, which may temporarily promote expansion of pioneer forest in the active channels. However, new geomorphic surfaces suitable for establishment of seedlings are no longer created because of altered peak flows and sediment supply, thereby threatening the recruitment opportunity and ultimate survival of their populations. Suppression of geomorphic disturbance also leads to the degradation of in-stream fauna. Channel straightening particularly simplifies geomorphic features of a river reach and diminishes longitudinal and lateral habitat diversity in its active channel. Flood control reduces inundation habitat and disrupts hydrologic connectivity between floodplain habitats (e.g., backwater and oxbow lakes), impacting fish and benthic invertebrates that require those habitats in their various life stages. A channel re-meandering experiment in the Shibetsu River, Hokkaido, demonstrates that the recovery of geomorphic dynamics can play significant roles in restoration of river ecosystems. Meandering reaches develop shallow edge habitat with low hydraulic stress along the inside of a convex, providing stable substrate for macroinvertebrate communities. Fallen trees provided by lateral erosion also promote macroinvertebrate colonization and become in-stream covers for fish communities. Geoecology in Japan as well as Europe and U.S. has long focused on vegetation pattern in alpine regions and has unexplored terrestrial and aquatic ecosystems in the vicinity of human activities. Knowledge in habitat dynamics and geomorphic processes is vital to ecosystem conservation and restoration. We believe that participation of geomorphologists is essential in future development of conservation and restoration strategies.