Large-scale anthropogenic river modifications have caused the loss of critical floodplain nursery habitats for riverine fish, leading to population declines. Restoration efforts have been implemented to recover these habitats, but with varying success. Understanding how larval and juvenile fish use habitats in dynamic river environments is essential for improving restoration strategies. We assessed ontogenetic shifts in habitat use by young-of-the-year (YOY) fishes in the lower Rhine, analysing 2,167 samples across 18 restored floodplains over three growing seasons (2018–2020). Five distinct nursery habitats were identified: (1) exposed, fast-flowing habitats with coarse substrate, (2) turbid, non-flowing areas with high turbidity and chlorophyll, (3) shallow, vegetated habitats with macrophytes and shoreline vegetation, (4) deeper, sheltered habitats with structural complexity, and (5) shallow, slow-flowing areas. Habitat use shifted significantly with ontogeny across species. Larvae generally preferred shallow habitats (50 cm depth), favouring fast-flowing areas (e.g., asp, barbel, ide) or deeper, non-flowing habitats (e.g., bream, zander). Our findings thus highlight the critical importance of habitat heterogeneity and connectivity for riverine fish biodiversity. Restoration strategies should prioritise the creation of a mosaic of shallow, low-velocity habitats for larvae, alongside deeper, fast-flowing or sheltered areas for juveniles. Additionally, the movement of rheophilic species from floodplain habitats to the main river channel emphasises the need for maintaining continuous connectivity between floodplains and the river.

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