This study investigates the impact of flow structure of different discharges on meander point bar morphology. We carried out mobile and terrestrial laser scanning campaigns before and after a flood on two sandy-bed point bars. Between the scans, the flow structure was examined using an Acoustic Doppler Current Profiler at three flow stages. The results indicated that a meander point bar both affects and in turn, is itself modified by the flow at different discharges. The lower flow stages also have a significant effect on point bar morphology, especially on deposition over the bar head. Secondary circulation is responsible for scroll bar formation on the point bar margin beyond the apex. Flow separation at the inner bank, by contrast, does not require secondary circulation, but is dependent on flow depth over the point bar. A sudden increase in depth beyond the point bar top causes decreased stream power over the bar tail. The flow separation and decreased stream power cause a slow flow zone and net deposition over point bar tail. The backwater effect, if evident, may strengthen the process. Thus, filling over the bar tail seems generic for point bars and independent on secondary flow. Chutes and chute bars, scroll bars, bar head filling and bar platform filling, by contrast, require special fluvio-morphological circumstances discussed in this paper. Whilst this paper confirms that the three-dimensional flow structure has a major effect on point bar morphology, the flow structure seems to depend on how the point bar affects the flow trajectory which, in turn, depends upon the flow stage. Finally, the shape of the bend and the grain size distribution control the impacts of the flow structure, leading to divergent morphologies of point bars with certain generic features. Copyright © 2012 John Wiley & Sons, Ltd.