Geoarchaeological investigations that were conducted, during the 1970s in pariticular, in various regions of Greece, show that the morphology of the landscape during the Neolithic Period differed considerably from today's. The rise in the sea level that took place at the end of the Ice Age (approximately 11,000 years before the present) continued during the whole of the Neolithic. The result was that small peninsulas originally connected to the mainland, such as the northern Sporades with Thessaly, were transformed into large or small islands.

In other regions, the sea-level was lower than it is today and allowed coastal settlements, which today are covered by the sea (e.g. Franchthi in Hermionid), to develop. At the estuaries of rivers, the continuous accumulation of silt had the opposite result, that is to extend the shoreline. Thus, coastal Neolithic settlements, such as Dimini in Volos, are today situated several kilometres away from the shoreline. The continuous accumulation of silt in lowland areas, such as those of eastern Macedonia and Thrace, brought about a rise in the ground level by several or even many metres, with the result that Neolithic settlements disappeared under erosion materials and alluvian deposits.

Pollen analyses and palaeobotanical research (study of floral remains) show that the climate during the Neolithic Period did not considerably differ from the modern climate. It was Mediterranean, with wet and slightly colder winters but dry, hot summers.

Geomorphology and climate had a direct effect on vegetation, and consequently the choice of location for habitation. It is believed that locations with maquis vegetation were preferred to woods, as they were easier to clear and to turn into profitable, arable lands which were of vital importance for the first farmers.