On the schist, gneiss and plutonic rocky coasts of the island group of Mykonos, Delos, and Rheneia, beachrocks are the main geomorphological sea-level indicators. The detailed mapping and depth measuring of the five distinct beachrock generations identified at 22 locations throughout the coast of the island group point to five corresponding sea-level stands at 4.80 ± 0.10 m, 3.70 ± 0.20 m, 2.40 ± 0.25 m, 1.55 ± 0.25 m, and 0.80 ± 0.10 m below mean sea level, during which each generation was formed. The submerged archaeological sea-level markers found on the coast of the three islands, combined with the recalibrated ages of previously published radiocarbon dating of beachrock cements and the dating of the relevant sea-level stands identified on the islands of the northern and central Cyclades, led to the dating of the Late Holocene relative sea-level changes along the island group coast. From the Late Neolithic period onward, the sea level has risen at continuously increasing rates, with an average value of 0.76 mm/year. The inferred dated sea-level stands enabled the palaeogeographic reconstruction of the seafront of the ancient city of Delos and the Delos Strait, thus revealing both the coastline evolution over time and navigation of the strait during antiquity. © 2023, The Author(s), under exclusive licence to Springer Nature Switzerland AG.