In response to challenges in land cover classification (LCC), many researchers have experimented recently with classification methods based on artificial intelligence techniques. For LCC mapping of the vegetated Asahi River in Japan, the current study uses deep learning (DL)-based DeepLabV3 module for image segmentation of aerial photographs. We modified the existing model by concatenating data on its resultant output port to access the airborne laser bathymetry (ALB) dataset, including voxel-based laser points and vegetation height (i.e. Findings revealed that the modified approach improved the accuracy of LCC greatly compared to our earlier unsupervised ALB-based method, with 25 and 35% improvement, respectively, in overall accuracy and the macro F1-score for November 2017 dataset (no–leaf condition). Finally, by estimating flow-resistance parameters in flood modelling using LCC mapping-derived data, we conclude that the upgraded DL methodology produces better fit between numerically analyzed and observed peak water levels.