The NaturaSat software integrates various image processing techniques together with vegetation data, into one multipurpose tool that is designed for performing facilities for all requirements of habitat exploration, all in one place. It provides direct access to multispectral Sentinel-2 data provided by the European Space Agency. It supports using these data with various vegetation databases, in a user-friendly environment, for, e.g., vegetation scientists, fieldwork experts, and nature conservationists. The presented study introduces the NaturaSat software, describes new powerful tools, such as the semi-automatic and automatic segmentation methods, and natural numerical networks, together with validated examples comparing field surveys and software outputs. The software is robust enough for field work researchers and stakeholders to accurately extract target units’ borders, even on the habitat level. The deep learning algorithm, developed for habitat classification within the NaturaSat software, can also be used in various research tasks or in nature conservation practices, such as identifying ecosystem services and conservation value. The exact maps of the habitats obtained within the project can improve many further vegetation and landscape ecology studies.