During the last decades, fluvial sediment cores have been used to reconstruct and model pollution trends, especially for the post-1945 period. Ecological changes have been rarely studied in such recent sediment archives due to low organic levels and high hydro-sedimentary dynamics. Here, we address the challenge of reconstructing ecosystem changes along highly anthropized rivers by analysing plant macrofossils (e.g. seeds, wood fragments, mosses), animal and abiotic remains (mainly iron slags) accumulated in side channels. The main objective is to determine whether this approach – inspired from palaeoecology – is reliable. Interestingly, macrofossil records offer a coherent history of the species habitats and biodiversity on different sites on either side of a bypassed section of the Rhône River (France). Three main hydro-ecological phases are identified, linked to river developments. (1) A lotic phase, before damming, is marked by various local riparian forest taxa: black alder and willow macrofossils were regularly found in the cores, while black poplar is not recorded, despite its historical presence. (2) A synchronous terrestrialization phase (transition from an aquatic to a terrestrial ecosystem) is highlighted on both side channels in the late 1970s, due to the bypassing of the river and the subsequent lowering of the water level. During this phase, nitrophilous plants (nettles) expanded on both sites. (3) Finally, the effects of restoration also appeared in fluvial sediment cores, marked by new aquatic flora and fauna macrofossil taxa since 2000. Overall, this research demonstrated the potential of studying macrofossils in side channel deposits to understand the post-1945 history of riparian habitats and biodiversity, and their evolution after developments and/or restoration actions. This macrofossil approach could be considered as a tool to supplement monitoring data and to better interpret wetland changes with regard to hydromorphological adjustments along a river system over decades or centuries.