Crete is part of the Hellenides mountain range created by the same tectonism that was responsible for the orogenesis of the Alps and the formation of the Mediterranean Sea during the first half of the Quaternary period about 40-20 million years ago. The land is constituted of three tectonic plates whose borders are located in the isthmus of Ierapetra and Rethymnon. The tectonic trenches were filled periodically by sea deposits which were transformed into limestone rocks and limestone and clay soil.

During the Mediterranean salinity crisis which started in the late Miocene and lasted two million years, successive deposits of evaporated minerals accumulated in the Mediterranean basin. The deposits of this period on Crete resulted in the formation of extensive plains, such as the Mesara plain which is rich in limestone sediment. The residues of this period appear in plants and sea microfossils which are found in the clay used in Minoan ceramics. These rocks also contain pieces of crystalline gypsum - or gypsum - a material often used by the Minoans in the construction of buildings, mainly in central Crete.

Towards the end of the Messinian age and at the beginning of the Pliocene epoch, that is 5 million years ago, the entire Mediterranean basin was flooded with Atlantic water. Towards the end of this geologic period regional tectonism gave rise to an island approximately equivalent to Crete. The heights of Psiloritis were elevated enough to experience a cold climate and the so-called stonemounts were created. The deposits of the late Pliocene are more or less uniform throughout the island, constituting one third of its surface. There is an obvious correlation between the Neogene rocks and the areas that were chosen for habitation, for these rocks were appropriate for stone quarrying and their soil is also of good quality. Important centres of Minoan civilization, such as Phaistos and Agia Triada are situated on a Plio-Pleistocene tectonic horst fault block.