Embracing smart irrigation management techniques empowers growers to irrigate with greater efficiency, thereby promoting sustainable agricultural production. In this context, growers often rely on crop evapotranspiration (ETc) as a key factor in making informed irrigation decisions, underscoring the significance of accurately determining and spatially mapping crop water status. Technological progress, exemplified by the emergence of unmanned aerial vehicles (UAVs), has brought about a revolutionary shift in agricultural monitoring. UAV platforms can capture high-resolution images with centimeter-level spatial accuracy and offer higher temporal coverage compared to satellite imagery. Considering these advancements, this study introduces a robust method for classifying water stress in cotton using a compact UAV platform and convolutional neural networks (CNN). The experiment was conducted at the USDA-ARS Cropping Systems Research Laboratory (CSRL) in Lubbock, Texas, where the cotton field was divided into 12 drip zones. The study included three replications to evaluate four irrigation treatments: “rainfed”, “full irrigation”, “percent deficit of full irrigation”, and “time delay of full irrigation”. The results demonstrated that the CNN model successfully classified the cotton water stress using the UAV-based RGB image, achieving an overall best prediction accuracy of approximately 91%. By segmenting the original cotton images into separate canopy and soil areas using morphological image processing methods, the authors also isolated and analyzed the individual contributions of these components to cotton water stress. Additionally, a random forest classifier revealed the relative importance of different image features in the classification process through feature importance analysis. These findings highlighted the state-of-the-art performance of the proposed system in cotton water stress classification and provided valuable insights into the key image features contributing to accurate classification. The authors concluded that integrating UAV-based RGB imagery and CNN models had great potential for assessing water stress in cotton.