Landscape evolution from the Early 1st millennium BCE to the mid-1st millennium CE is poorly documented around major archaeological sites in Crete. In a previous publication, the general landscape configuration in the vicinity of ancient Phaistos was reconstructed using a palaeoenvironmental approach, from the Proto-Palatial period (ca. 2000 BCE) to the Late-Proto Geometric period (ca. 8th cent. BCE). However, the physiography of the landscape, its hydrology and vegetation history remained uncertain for the later archaeological periods. In the present study, additional radiocarbon dates (8) together with pollen, mollusc and sedimentological analyses (CM diagram) were conducted on previously documented sediment cores. These new results enable us to reconstruct in greater detail the landscape history from the Early Archaic period to Late Byzantine times. The results indicate the continuous presence of swampland from the Proto-Geometric period (10th cent. BCE) probably until the initial stages of the Classical period (5th cent. BCE). Subsequently, during the Classical and Hellenistic periods, there was a short interval of alluvial input of terriginous sediments (not exceeding two centuries in duration) which is directly linked with the complete drying up and drainage of the swampland. We address the issue of the possible climatic origin of this abrupt hydrological change, especially in relation to regional climate change and the sedimentary history of adjacent rivers and streams. Tectonic activity in the area is also an important factor and can be invoked as a potential environmental influence. Anthropogenic factors are also considered, even though there is no direct archaeological evidence of drainage in the western Messara Plain during the Archaic and Classical periods. Finally, from Roman times to the Early Byzantine period, floodplain development prevailed in the area and ponds formed locally, in particular from the Late Hellenistic to Early Byzantine periods; this was related to the climatic conditions of the Roman Warm period. Pollen analysis reveals an open forested landscape during the time interval under investigation, within which domesticated plants such as Olea (olive) were present. However, the representation of Olea decreases continuously from the Late Geometric period to Byzantine times, probably indicating much lower intensity of land use than during Minoan times and possibly also related to the generally colder climatic conditions in Crete from the 8th cent. BCE until the 1st Cent. CE. During this latter interval, there is also the first pollen analytical evidence of Vitis sp.