The grain-scale morphology and size distribution of sediments are important factors controlling the erosion efficiency, sediment transport and the aquatic ecosystem quality. In turn, characterizing the spatial evolution of grain size and shape can help understand the dynamics of erosion and sediment transport in coastal, hillslope and fluvial environments. However, the size distribution of sediments is generally assessed using insufficiently representative field measurements, and determining the grain-scale shape of sediments remains a real challenge in geomorphology. Here we determine the size distribution and grain-scale shape of sediments located in coastal and river environments with a new methodology based on the segmentation and geometric fitting of 3D point clouds. Point cloud segmentation of individual grains is performed using a watershed algorithm applied here to 3D point clouds. Once the grains are segmented into several sub-clouds, each grain-scale morphology is determined by fitting a 3D geometrical model applied to each sub-cloud. If different geometrical models can be tested, this study focuses mostly on ellipsoids to describe the geometry of grains. G3Point is a semi-automatic approach that requires a trial-and-error approach to determine the best combination of parameter values. Validation of the results is performed either by comparing the obtained size distribution to independent measurements (e.g., hand measurements) or by visually inspecting the quality of the segmented grains. The main benefits of this semi-automatic and non-destructive method are that it provides access to (1) an un-biased estimate of surface grain-size distribution on a large range of scales, from centimeters to meters; (2) a very large number of data, mostly limited by the number of grains in the point cloud data set; (3) the 3D morphology of grains, in turn allowing the development of new metrics that characterize the size and shape of grains; and (4) the in situ orientation and organization of grains. The main limit of this method is that it is only able to detect grains with a characteristic size significantly greater than the resolution of the point cloud.