Floodplain channels of rivers 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 multi-site data collected over 20 years in eight restored sectors of the Rhône River. Results show that habitat use by fish is mainly related to spatial effects. As expected, rheophilic species were more abundant in lotic stations and limnophilic species in lentic ones. In addition, we identified an euryecious guild, grouping youngs of the year taxa, that used all types of habitats and particularly lentic floodplain channels with short life-span. Temporal effects combine (1) the effect of restoration, particularly in floodplain channels for which the connectivity regime was modified, (2) the effect of high flows upon the habitat use by fish that reinforces the nursery and refuge functions of floodplain channels. To conclude, our results demonstrate the importance of restoring habitat diversity and connectivity because habitats may have complementary functions for fish. Furthermore, our results also highlight that it is essential to account for temporal variations in order to better estimate the potential effects of restoration on river and their floodplains.