The alluvia of the Ntem, Nyong and Sanaga fluvial systems in southern Cameroon recorded repeated fluvial activity fluctuations during the Late Pleistocene, including the last glacial maximum (LGM), the beginning of the African Humid Period and the northern hemispheric Bølling-Allerød. We applied a multi-proxy approach on alluvial stratigraphies dated between 22.4 and 13.0 cal ka BP, including remote sensing, sedimentological and morphogenetic methods, phytoliths, sponge spicules, 14C and δ13C data. A distinct NE–SW gradient of landscape and fluvial dynamics around the LGM can be drawn, with evidence for the persistence of extended fluvial rainforest refuges only in the Ntem catchment. The Sanaga and Nyong catchment areas were characterized by frequent channel migrations, floodplain reorganization and unstable vegetation subject to fire, including grasslands, woodlands, and gallery forests with bamboo thickets. In spite of increasing rainfall after 16.4 cal ka BP, persisting landscape instability played the major role for fluvial system dynamics, floodplain transformations and vegetation development until 13.0 cal ka BP, before a general landscape stabilization and rainforest expansion set in at the beginning of the Holocene.