The extensive modifications in the River Rhine resulted in the severe decline or even loss of migratory fish species, typical for European lowland river systems, such as Atlantic salmon (Salmo salar) and European sturgeon (Acipenser sturio). In addition, the numbers of other potamodromous, rheophilic species, such as European barbel (Barbus barbus) and Nase (Chondrostoma nasus) have significantly reduced. Since the 1990s, authorities in the Netherlands have reconstructed numerous floodplains to improve the ecological quality of the river systems. This resulted in positive changes to water quality and habitat variability, but not to the expected recovery of rheophilic fish species, an indicator for good ecological quality. We expect that the slow recovery of rheophilic fish populations is mainly caused by insufficient presence and accessibility of those floodplain habitats that function as nursery areas for young fish. To assess the relation between the quantity and quality of these floodplain nursery areas with rheophilic fish recruitment, a large-scale, 4-year (2017-2020) comparative study was initiated. In 2017 450 juvenile fish communities in 59 floodplain water systems along four main branches of the Rhine, covering 351 river km were sampled in a wide-range of floodplain and river habitats. In addition, 39 abiotic and biotic environmental variables were measured. In the first year of this study we caught ca. 135,0000 fish, belonging to 37 species. The eurytopic species Perca fluviatilis, Rutilus rutilus and Abramis brama were most common, accounting for 56% of the total catch. Rheophilic species Leucistus idus, Aspius aspius, Alburnoides bipunctatus and Chondrostoma nasus made up only 29% of the catch. Our main preliminary conclusion is that water conductivity, river-floodplain connectivity and especially habitat variability were the main positive drivers of juvenile rheophilic fish abundance in the floodplains, suggesting that in future floodplain reconstructions specific attention should be paid to these aspects.