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This methods paper details the first attempt at monitoring bank erosion, flow and suspended sediment at a site during flooding on the Mekong River induced by the passage of tropical cyclones. We deployed integrated mobile laser scanning (MLS) and multibeam echo sounding (MBES), alongside acoustic Doppler current profiling (aDcp), to directly measure changes in river bank and bed at high (˜0.05 m) spatial resolution, in conjunction with measurements of flow and suspended sediment dynamics. We outline the methodological steps used to collect and process this complex point cloud data, and detail the procedures used to process and calibrate the aDcp flow and sediment flux data. A comparison with conventional remote sensing methods of estimating bank erosion, using aerial images and Landsat imagery, reveals that traditional techniques are error prone at the high temporal resolutions required to quantify the patterns and volumes of bank erosion induced by the passage of individual flood events. Our analysis reveals the importance of cyclone-driven flood events in causing high rates of erosion and suspended sediment transport, with a c. twofold increase in bank erosion volumes and a fourfold increase in suspended sediment volumes in the cyclone-affected wet season. Copyright © 2016 John Wiley & Sons, Ltd.