The study examines the relationship between floodplain aquatic macroinvertebrates and sector-scale parameters such as geomorphology and history of regulation. The assemblages of six groups of invertebrates (Molluscs, Crustaceans, Ephemeroptera, Odonata, Trichoptera, and Coleoptera) were compared in various types of former channels from two contrasting but adjacent floodplain sectors: (1) the Jons sector of the Rhǒne River where successive meandering and braiding phases has left diversified fluvial forms in the landscape but where the main river is now embanked, and (2) the unregulated Ain River sector where the river is still actively meandering, although this process is being slowed by incision. The results demonstrate little difference in faunal composition between the two sectors but a significant difference in faunal structure. In the Rhǒne floodplain, there was a clear distinction between the faunal assemblages together with a high taxa richness at the scale of the sector (dominance of the beta diversity). In the Ain floodplain, the faunal assemblages were overlapping and the taxa richness was high at the sample scale (alpha diversity). Sector-scale spatial patterns of the faunal assemblages along former channels were also distinct: between-channel heterogeneity dominated in the Rhǒne, whereas within-channel heterogeneity dominated on the Ain. These results stress the influence of geomorphological and historical determinants on the floodplain communities and, conversely, the relevance of macroinvertebrate assemblages for the assessment, at the landscape scale, of aquatic systems within the floodplains.