Posidonia oceanica meadows are a species of seagrass highly dependent on rocks for their survival and conservation. In recent years, there has been a concerning global decline in this species, emphasizing the critical need for efficient monitoring and assessment tools. While deep learning-based semantic segmentation and visual automated monitoring systems have shown promise in a variety of applications, their performance in underwater environments remains challenging due to complex water conditions and limited datasets. This paper introduces a framework that combines machine learning and computer vision techniques to enable an autonomous underwater vehicle (AUV) to inspect the boundaries of Posidonia oceanica meadows autonomously. The framework incorporates an image segmentation module using an existing Mask R-CNN model and a strategy for Posidonia oceanica meadow boundary tracking. Furthermore, a new class dedicated to rocks is introduced to enhance the existing model, aiming to contribute to a comprehensive monitoring approach and provide a deeper understanding of the intricate interactions between the meadow and its surrounding environment. The image segmentation model is validated using real underwater images, while the overall inspection framework is evaluated in a realistic simulation environment, replicating actual monitoring scenarios with real underwater images. The results demonstrate that the proposed framework enables the AUV to autonomously accomplish the main tasks of underwater inspection and segmentation of rocks. Consequently, this work holds significant potential for the conservation and protection of marine environments, providing valuable insights into the status of Posidonia oceanica meadows and supporting targeted preservation efforts