River bed materials serve multiple environmental functions as a habitat for aquatic invertebrates and fishes. At the same time, the particle size of the bed material reflects the tractive force of the flow regime in a flood and provides useful information for flood control. The traditional river bed particle size surveys, such as sieving, require time and labor to investigate river bed materials. The authors proposed a method to classify aerial images taken by unmanned aerial vehicle (UAV) using convolutional neural networks (CNN), our previous study showed that terrestrial riverbed material could be classified with high accuracy. In this study, we attempted to classify riverbed materials distributed in shallow waters where the bottom can be seen from UAVs. After training the CNN to classify the images with the same grain size as being in the same class even if the surface flow types taken overlapping the riverbed material were different, the total accuracy reached 90.3%. Moreover, the proposed method was applied to the wide-ranging area to determine the distribution of the particle size. In parallel, the microtopography was surveyed using Lidar-UAV, and the relationship between the microtopography and particle size distribution was discussed. In the steep section, coarse particles were distributed and formed a rapid. Fine particles were deposited on the upstream side of those rapids, where the slope had become gentler due to the damming. There was good agreement between the microtopographical trends and the grain size distribution.