The paper reports on a synthesis of pollen analyses and main archaeobotanical studies carried out on Early, Middle and Late Holocene sites from Sai Island in the Nile River (ancient Upper Nubia, present northern Sudan). Multidisciplinary archaeological studies focused on the transitions from hunting-fishing-gathering to pastoralism and later to agro-pastoralism in this area. New palynological data were obtained from two sites located on the eastern side of the island: an Early Holocene occupational level of a ‘Khartoum Variant’ foraging site (8-B-10C, Level 2; c. 7600–7200 BC), and a Middle/Late Holocene site dating to the Pre-Kerma/Kerma period (8-B-10A; the later phase is dated c. 1800–1600 BC). These data integrate the results obtained from two other sites located on the western side of the island (sites 8-B-76 and 8-B-81). Despite the poor preservation of pollen, the integration of data from the studied sites provides information on the environmental changes and potential for plant exploitation in the eastern Sahelian-Saharan region. A substantial environmental diversity between the west and east sides of Sai Island emerges, revealing that in the late Early Holocene and first part of the Middle Holocene the land near the river was characterised by a mosaic of habitats, with dramatic floods on the eastern side and seasonal dried-up areas on the western side. This region supplied water even during the dry climatic phases and provided humans with mosaic habitats within short distances, giving access to plants (useful for food and other purposes) which lived in swamps and marshes, wooded savannahs, grasslands or desert savannahs.