Water is essential for any crop production. Lack of sufficient supply of water supply causes abiotic stress in crops. Accurate identification of the crops affected by drought is required for achieving sustainable agricultural yield. The image data plays a crucial role in studying the crop's response. Recent developments in aerial-based imaging methods allow us to capture RGB maize data by integrating an RGB camera with the drone. In this work, we propose a pipeline to collect data rapidly, pre-process the data and apply deep learning based models to segment drought affected/stressed and unaffected/healthy RGB maize crop grown in controlled water conditions. We develop an ensemble-based framework based on U-Net and U-Net++ architectures for the drought stress segmentation task. The ensemble framework is based on the stacking approach by averaging the predictions of fine-tuned U-Net and U-Net++ models to generate the output mask. The experimental results showed that the ensemble framework performed better than individual U-Net and U-Net++ models on the test set with a mean IoU of 0.71 and a dice coefficient of 0.74. © 2022 IEEE.