Naxos mainly consists of a series of deformed and metamorphosed Mesozoic platform sediments, which surround a structural dome of Hercynian gneisses basement.The island also is comprised of magmatic rocks of various ages and deformation, allochthonous Mesozoic molassic sediments  and pyrogenic rocks, and also Pliocene and Pleistocene sediments derived from the eroding dome.

The main hydrogeologic units of Naxos are the alluvium and the crystalline rocks. This research concentrates mainly to the crystalline rocks (schists, gneisses, migmatite, granodiorite and marbles) that compose the major part of Naxos. These rocks have a low primary permeability; the ability to transmit water through them depends on a fracture and/or solution-induced secondary permeability.