The Greek island of Nisyros, located in the Aegean Sea and part of the Cyclades Arc, is known for its hydrothermal alterations and phreatic explosions, forming the Stefanos crater. Sudden explosions, like the one in 1887, pose a significant hazard. The aim of this work is to identify and locate the various degrees of hydrothermal alteration with a combination of point-wise rock sampling and geospatial data analysis. For the petrological study different lithologies at different degrees of hydrothermal alteration are sampled and analyzed with the XRF. Geospatial analysis is realized by drones equipped with optical and thermal cameras. The data are processed and analyzed with Metashape and ArcMap software. Photogrammetric processing of the drone data allows generating orthomosaics of the Stefanos crater with a resolution of 2.94 cm/pix. The infrared data show an increased apparent temperature at the fumarole fields of up to 50°C. Using Principal Component Analysis (PCA), the geological units are classified in temporal lake (0), outer crater wall (1), upper crater wall (2), tuff layer (3), lower crater wall (4), sediments – divided into debris flow (5A) and crater ground (5B), a mixture of lower crater wall and fumarole crust (6) and fumarole crust (7). The degree of hydrothermal alteration increases from unit 0 to 7, with unit 7 being the most altered, covering an area of approximately 1.1e+4 m2. The classification and XRF analysis are used to determine the relationship between temperature, distance to the crater center, sulfur content and degree of alteration of various lithologies.