The increased rock-weathering during the Quaternary period led to erosion and consequently to the deposition of a great quantity of material in the Mesara valley and in other higher valleys, such as Omalos, Nida and Lasithi. The intensive agricultural activity and deforestation during the early Bronze Age led to the advanced erosion of the soil, which, as in mainland Greece, is observed in the slopes and the beds of the valleys. The soils that occur most commonly in Crete are various kinds of clay earth and dark rocky soils on hard limestone deposits. The most appropriate soils for cultivation are in regions with flysch and slate, particularly in water valleys and plateaux where erosion is more obvious. Conditions favouring settlement occur in the regions of Ida, Mochlos, Neapoli, Siteia and Ano Zakros. Specifically, flysch which occurs in the Asterousia mountains, Anogeia, Gonies, Ida and the Lasithi plateau is always accompanied by soil of good quality which can be compared to that of Neogene rocks.

The Neogene soils which cover one third of the surface of Crete constitute the most appropriate substratum for agricultural exploitation. These soils resulted from earlier deposits which were concentrated on the seabed and formed an extensive nappe of sea marl and conglomerate rocks. Large areas of soft limestone and marl are found in the northern and central regions, east of Ida, on the hills of Phaistos, in Knossos and in western Mesara. As for southern Crete, soft limestone and sea marl are found at the foot of the Asterousia mountains and Ida. The pure limestone soils are ideal for retaining water during summertime and in transforming organic residues into carbon dioxide which is useful in cultivations.

The conglomerate soils are less appropriate for farming because they are hard and are found in rocky regions. In such infertile land, cultivation is really only possible in valleys or plateaux, that is where there is adequate moisture and rich erosion products, as in the hilly regions north of the Mesara valley, in the Amari valley, the isthmus of Ierapetra, to the east of the peak of Dhikti and in various regions of eastern Crete, particularly in Siteia, Praisos, the Toplou peninsula and in the southern peaks of eastern Crete. Conglomerate soils also cover extensive areas of eastern Crete thus rendering the region inappropriate for cultivation unlike central and northern Crete.