Japan was hit by typhoon Hagibis, which came with torrential rains submerging almost eight-thousand buildings. For fast alleviation of and recovery from flood damage, a quick, broad, and accurate assessment of the damage situation is required. Image analysis provides a much more feasible alternative than on-site sensors due to their installation and maintenance costs. Nevertheless, most state-of-art research relies on only ground-level images that are inevitably limited in their field of vision. This paper presents a water level detection system based on aerial drone-based image recognition. The system applies the R-CNN learning model together with a novel labeling method on the reference objects, including houses and cars. The proposed system tackles the challenges of the limited and wild data set of flood images from the top view with data augmentation and transfer-learning overlaying Mask R-CNN for the object recognition model. Additionally, the VGG16 network is employed for water level detection purposes. We evaluated the proposed system on realistic images captured at disaster time. Preliminary results show that the system can achieve a detection accuracy of submerged objects of 73.42% with as low as only 21.43 cm error in estimating the water level.