A large share of surface water resources in Sahelian countries originates from Guinea’s Fouta Djallon highlands, earning the area the name of “the water tower of West Africa”. This paper aims to investigate the recent dynamics of the Fouta Djallon’s hydrological functioning. The evolution of the runoff and depletion coefficients are analyzed as well as their correlations with the rainfall and vegetation cover. The latter is described at three different space scales and with different methods. Twenty-five years after the end of the 1968–1993 major drought, annual discharges continue to slowly increase, nearly reaching a long-term average, as natural reservoirs which emptied to sustain streamflows during the drought have been replenishing since the 1990s, explaining the slow increase in discharges. However, another important trend has been detected since the beginning of the drought, i.e., the increase in the depletion coefficient of most of the Fouta Djallon upper basins, as a consequence of the reduction in the soil water-holding capacity. After confirming the pertinence and significance of this increase and subsequent decrease in the depletion coefficient, this paper identifies the factors possibly linked with the basins’ storage capacity trends. The densely populated areas of the summit plateau are also shown to be the ones where vegetation cover is not threatened and where ecological intensification of rural activities is ancient.