This study aims to reconstruct the Holocene fluvial history of the Tremithos river, south central Cyprus and examine linkages to regional and local archaeological records. Three stratigraphic profiles (Sp1, Sp2 and Sp3) located in the lower valley have been investigated using sedimentology and magnetic parameters. The 14C dating of 10 samples reveals mid-Holocene ages for Sp1 and Sp2, while the upper most part of Sp3 can be attributed to the early to mid-Holocene. Two main phases of vertical accretion have been recognised: the first, recorded in the lower most part of Sp3, could not be dated but might relate to the late Glacial period. It is not associated with any archaeological artefacts. The second, recorded in all profiles, dating from ca. 5000 to ca. cal 2800 BC, spans the Late Neolithic Sotira (cal 4800/4000 BC) and Late Chalcolithic (cal 2900–2500 BC) cultures. The sediments of Sp1 and Sp2 are up to 8–10 m thick and mainly composed of fine material. However, an intercalated phase of coarse sediment has been identified at the beginning of the third millennium BC, indicating a sudden change in river dynamics, potentially associated with the 5.2 ka rapid climate change regional event. Typical mid-Chalcolithic (ca. cal 3300–3050 BC) ceramics found in a palaeosol in Sp2 indicate for the first time human occupation of the Tremithos river terraces. Two other palaeosols have also been recognised in Sp3 and radiocarbon dated to ca. cal 5600–4100 BC and ca. cal 2900–2600 BC, respectively. These results make it possible to propose a palaeogeographic reconstruction of the Holocene evolution in the Tremithos valley and to make a preliminary assessment of the relative roles of tectonics, climate and anthropogenic forcing.