1. Large river floodplains contain a high diversity of habitats and species but are highly threatened by human activities. River floodplain restoration is increasingly undertaken to reverse biodiversity loss and enhance ecosystem services. 2. Few studies have examined the consequences on the biota of restoring lateral connectivity, a key variable that represents the exchange of materials and organisms between the river and its floodplain. We developed models to describe the richness and abundance of aquatic macroinvertebrates in 18 channels of the Rh^one floodplain and predict how restoration (i.e. the increase in lateral connectivity of floodplain channels) should alter the native and alien communities. 3. Models quantified how richness and abundance decrease for lentic taxa and increase for lotic and alien taxa with higher connectivity between the floodplain channels and the main channel. Predicted changes were weakly related to overall observed changes when all restored channels were combined, but consistent with observed changes when floodplain channels were grouped by restoration type. We highlighted that restoration interventions modifying lateral connectivity induced a change of lentic and lotic taxa richness in accordance with the predictions. Richness of alien taxa was favoured by restoration more than predicted; however, no interaction between alien species changes and native species was detected after restoration. 4. Restoration of the ecosystem predictably transformed native communities and encouraged alien species, at least over the 4 years studied. Our findings demonstrate that lateral connectivity is a key variable driving macroinvertebrate communities in large river floodplains and that the response of macroinvertebrates to restoration of a disturbance-driven ecosystem can in part be predicted. Therefore, the outcome of restoration programmes can be optimised by quantifying lateral connectivity before and after restoration.