Although past climate change is well documented in West Africa through instrumental records, modeling activities, and paleo-data, little is known about regional-scale ecosystem vulnerability and long-term impacts of climate on plant distribution and biodiversity. Here we use paleohydrological and paleobotanical data to discuss the relation between available surface water, monsoon rainfall and vegetation distribution in West Africa during the Holocene. The individual patterns of plant migration or community shifts in latitude are explained by differences among tolerance limits of species to rainfall amount and seasonality. Using the probability density function methodology, we show here that the widespread development of lakes, wetlands and rivers at the time of the "Green Sahara" played an additional role in forming a network of topographically defined water availability, allowing for tropical plants to migrate north from 15 to 24° N (reached ca. 9 cal ka BP). The analysis of the spatio-temporal changes in biodiversity, through both pollen occurrence and richness, shows that the core of the tropical rainbelt associated with the Intertropical Convergence Zone was centered at 15-20° N during the early Holocene wet period, with comparatively drier/more seasonal climate conditions south of 15° N.