Nisyros exclusively comprises volcanic products deposited above a substrate of Mesozoic limestone and Neogene sediments. Existence of this substrate is evidenced at the surface by the presence of xenoliths consisting of Neogene clays and Mesozoic limestone.

The later ones were cut by the deep geothermal exploration borehole Ν-1 (Geotermica It., 1983), which encountered their peak at 600m deep below the sea level. The islets of Strongili, Yali, Ag. Antonios, Pyrgousa, Pahia and Kandeleousa (or Fanari) are located close to Nisyros. With the exception of the latter, being the remotest and consisting of reef limestone, all the others exclusively comprise of volcanites.

The following descriptions apply to the area’s geological formations, starting from the islets and proceeding from older to earlier formations. Numbers in parentheses correspond to the formations in the geological map legend.