In large river floodplains, the availability of trophic resources to the fish fauna is highly variable as a consequence of seasonal environmental change and habitat diversity. Young-of-the-year fishes (YOY) must find suitable habitats to settle, feed and survive. However, very few in-depth studies are available about the food preferences of the young fishes during their first growing season. Here, we investigated the composition of planktonic assemblages and the YOY diet of three generalist fish species Alburnus alburnus (Linnaeus, 1758), Squalius cephalus (Linnaeus, 1758) and Pseudorasbora parva (Temminck & Schlegel, 1846) from four floodplain sites of the French Upper Rhône River. More specifically, we studied their temporal and spatial variations in relation to five environmental variables: hydrology, dissolved oxygen, primary production, water temperature and conductivity. Stable flow conditions and the associated temperature and conductivity strongly structured the phytoplankton community in the floodplain channels, whereas water movements within channels and dissolved oxygen concen- trations were significantly correlated to the zooplankton composition. A zooplankton density above ≈100 ind L−1 allowed the initiation of a YOY diet mainly based upon zooplankton for the three fish species. When zooplankton densities were insufficient, all three species used phytoplankton as their main food resource. Finally, the diet overlaps between species, differed significantly between sites. The study highlights the need to examine the diet of juvenile fishes and environmental variables in the floodplains.