River floodplain channels can serve as reproduction, nursery or refuge areas for fish. Although the complementary use of floodplain and main channels is known, few studies attempted to quantify this use and even fewer analysed its controlling factors. The objectives of this study are (1) to describe the spatio-temporal use of floodplain habitats and to identify their roles as complementary habitats for fish and (2) to analyse how abiotic variations and their modifications under restoration impact habitat use by fish. To meet these objectives, we analysed (Principal Components Analysis and Coinertia Analysis) multi-site data collected over 20 years in eight main channels and 23 floodplain channels of eight restored sectors of the French Rhône River. Results show that habitat use by fish is mainly related to spatial effects, with 37 % of within-sector variance in taxonomic assemblages explained by the stations. As expected, rheophilic species were more abundant in lotic stations and limnophilic species in lentic ones. In addition, we identified an euryecious guild, grouping young of the year taxa (roach, gudgeon, chub, bleak) that used all types of habitats and particularly lentic floodplain channels with short life-span. Temporal effects (with ~10 % of the variance explained by years) combine (1) the effect of restoration, that increased the diversity of fish assemblages across the floodplain, with stronger changes in floodplain channels whose connectivity regime was modified, (2) the effect of high flows on fish habitat use, that reinforces the nursery and refuge functions of floodplain channels. Our results demonstrate the importance of restoring the diversity of habitats and connectivity because floodplain habitats have complementary functions for fish. Furthermore, our results also suggest to account for temporal variations in order to better estimate the potential effects of restoration on river and their floodplains.