Late Pleistocene beach deposits in 22 selected sites around Cyprus demonstrate the vertical changes in the Earth’s crust in that island over the last 125 ka. The beach/shallow-marine deposits were observed on the abraded coastal cliffs at 3–22 m above the present sea-level. They overlie Pliocene marls, and some of them contain the Senegalese marine gastropods Persististrombus latus, Bursa granularis and Conus ermineus that no longer live in the Mediterranean. These are index fossils for the Marine Isotope Stage (MIS) 5e in the Mediterranean and, as such, suggest an uplift of up to 15.5 m over about the last 125 ka: that is a maximal rate of 0.12 mm a⁻¹. These findings are in accordance with Holocene beachrocks, abrasion platforms, wave notches and Roman/Byzantine fish tanks that retained their elevations, and thus enable the reconstruction of the coast encountered by the early colonizers. While the maximal uplift since the early Holocene has been minor and did not exceed 1.2–1.5 m, the sea-level changes have reached 40–50 m. The transition between the impermeable Pliocene marls and the porous Late Pleistocene deposits above them is the origin of freshwater springs and associated vegetation. The early colonizers seemed to recognize the potential of that essential permanent source of water and excavated wells, the earliest wells known so far. The locations of the Early Neolithic settlements (Mylouthkia and Akanthou) adjacent to visible water springs along the coastal cliffs may not be incidental. Not surprisingly, recent wells dug in the coastal Pleistocene deposits rely on the very same hydrological setting.