We collected orthophotos of Paleochori Bay, Milos, Greece in 2018 by drone (Orthophotos.zip) and stitched those images together to obtain a high-resolution, georeferenced photographic image (Paleochori_Composite_Photo.tif). This image was used for further processing in ArcGIS to generate a 1:3300 scale map of the seafloor in Paleochori Bay (tjom_a_1748131_sm0990.pdf) with native shapefiles and layer files (Shapefiles.zip), showing the distribution of white microbial mats, former microbial mats, sea grass and “normal” sand down to a depth of 15 m. The georeferenced photographic image allows to obtain GPS coordinates for any point of interest in Paleochori Bay and thus, allows to target specific locations for data collection, rather than resorting to vague site descriptions, as has been the practice in the past. With aid from the georeferenced photo of Paleochori Bay, 150 sea floor temperatures were measurements by Scuba divers (Temperature_measurments.xlsx) to evaluate the temperature distribution in the bay, in order to further the overall understanding of the hydrothermal system.