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Multi-temporal analysis of river-floodplain processes is a key tool for the identification of reference conditions or benchmarks and for the evaluation of deviations or deficits as a basis for process-based river restoration in large modified rivers. This study developed a methodology for benchmarking fluvial processes at river segment level, focusing on those interrelations between morphodynamics (aggradation, erosion, channel shift) and vegetation succession (initial, colonization, transition) that condition habitat structure. Habitat maps of the free-flowing Upper Rhine River downstream from Iffezheim dam (France-Germany border) were intersected with a geographic information system-based approach. Patches showing trajectories of anthropization, changeless, progression and regression allowed for the identification of natural and human-induced processes over almost 200 years. Before channelization, the riverine system was characterized by a shifting habitat mosaic with natural heterogeneity, high degree of surface water connectivity and equilibrium between progression and regression processes. On the other hand, the following 175 years of human interventions led to severe biogeomorphologic deficits evidenced by loss of natural processes and habitat heterogeneity, hydrological disconnection between the river and its floodplain and imbalance of progression versus regression dynamics. The main driving forces of change are found in hydromorphological impacts (channelization, regulation and hydropower plant construction). Regression processes are now almost absent and have to be the objective of process-based river restoration measures for the studied river-floodplain system. A sustainable view on water management and river restoration should aim at a more resilient riverine system by balancing the recovery of natural processes with societal needs. Copyright © 2016 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]