Long-term changes (river incision, climate changes and groundwater overuse) induce increasing groundwater depletion and drought frequency in flood- plains. To evaluate the effect of drought on functioning of wetlands and their interstitial zones, we studied the intersti- tial communities at seven stations located in five former channels of the Rhône River. Change in interstitial assem- blages was assessed over a 32-year period in one wetland and over the entire floodplain between 1987 and 2010, at depths of 50 and 100 cm within the sediment. Over the 32- year period, we highlighted some links between environ- mental changes and variations in interstitial assemblages: a decrease in abundance and diversity of the hypogean fauna and a reverse pattern for Ephemeroptera and Cladocera. At the floodplain scale, several changes in habitat characteris- tics were observed and two drying modalities were identi- fied: the formation of isolated pools and the complete disappearance of surface water. In isolated pools, the low turnover of surface water promoted a decrease in water quality, an increase in the abundance of benthic invertebrates in the interstitial habitat and a decrease in the abundance of hypogean invertebrates. In completely dried-out sites, the abundance and diversity of benthic taxa decreased, while the hypogean fauna remained dominant. These results demon- strate that interstitial assemblages are affected by long-term changes (river incision and climate changes). The local geo- morphology and the resulting drying modalities control the responses of interstitial assemblages.