Despite more than 25 years of research, the spatial and temporal variability of hydrothermal venting in Paleochori Bay remains poorly constrained because there are no reliable repeat measurements at discrete locations. Using a georeferenced photographic map of Paleochori Bay (https://doi.org/10.1594/PANGAEA.915881), scuba divers collected 168 porewater and seawater samples inside and outside of the bay and exact GPS coordinates were recorded for each sample. The GPS coordinates of the sampling locations should provide a foundation for future research in Paleochori Bay by enabling reliable repeat measurements. The dataset was combined with the temperature measurements previously reported (https://doi.org/10.1594/PANGAEA.915881) and contains chemical, isotopic data, as well as water depth and sediment color. All porewater samples were taken at a sediment depth of 0.1 m.