Overflow-driven lateral connectivity significantly influences the spatial distribution and diversity of floodplain habitats and biota. Proper understanding of lateral connectivity in floodplain and backwater channels is therefore critical for assessment of river quality and for targeting management or restoration actions. In this study, we present a methodological framework for spatial and temporal assessments of overflow-driven lateral connectivity at two spatial scales: bypass reach and backwater channel. Firstly, we compute the relative elevations, as well as overflow discharge, duration, and frequency using a simple, raster-based method that uses a LiDAR digital elevation model (DEM), rating curves, and streamflow time series. Subsequently, we analyse the accuracy of this approach with respect to the accuracy of a DEM and evaluate its further applications. Altogether, four 10-km-long bypass reaches and 11 backwater channels are analysed, located along the Rhone River corridor in France. The results proved the precision of the method to be affected by the LiDAR DEM accuracy, which was on average more precise in a typically homogeneous floodplain setting rather than for backwater channel plugs with pronounced topographic complexity and usually riparian forest canopy. Amongst the four studied reaches, Bregnier Cordon proved to have the greatest flooding dynamics, followed by Belley and Chautagne. The hydrological connectivity pattern of Pierre Benite differed significantly. Three longitudinal patterns of hydrological connectivity of backwater channels displayed stepwise advancement of the water. The presented results can be used to assess ecological potential of floodplain habitats and their historic and prospective evolution through time. Copyright (c) 2014 John Wiley & Sons, Ltd.