The use of uncrewed aerial vehicle to map the environment increased significantly in the last decade enabling a finer assessment of the land cover. However, creating accurate maps of the environment is still a complex and costly task. Deep learning (DL) is a new generation of artificial neural network research that, combined with remote sensing techniques, allows a refined understanding of our environment and can help to solve challenging land cover mapping issues. This research focuses on the vegetation segmentation of kettle holes. Kettle holes are small, pond-like, depressional wetlands. Quantifying the vegetation present in this environment is essential to assess the biodiversity and the health of the ecosystem. A machine learning workflow has been developed, integrating a superpixel segmentation algorithm to build a robust dataset, which is followed by a set of DL architectures to classify 10 plant classes present in kettle holes. The best architecture for this task was Xception, which achieved an average F1-score of 85% in the segmentation of the species. The application of solely 318 samples per class enabled a successful mapping in the complex wetland environment, indicating an important direction for future health assessments in such landscapes.