Multiproxy analysis of a well-dated 25 ka lake sediment sequence from Lake Challa, on the eastern flank of Mount Kilimanjaro (East Africa), reveals the climatic controls that govern both the lake's paleohydrology and the climate-proxy record contained in the mountain's receding ice cap. The oxygen isotope record extracted from diatom silica (δ18Odiatom) in Lake Challa sediments captured dry conditions during the last glacial period and a wet late-glacial transition to the Holocene interrupted by Younger Dryas drought. Further, it faithfully traced gradual weakening of the southeastern monsoon during the Holocene. Overall, δ18Odiatom matches the branched isoprenoid tetraether (BIT) index of rainfall-induced soil runoff, except during 25–22 ka and the past 5 k.y. when insolation forcing due to orbital precession enhanced the northeastern monsoon. This pattern arises because during these two periods, a weakened southeastern monsoon reduced the amount of rainfall during the long rainy season and enhanced the opposing effect of evaporation intensity and/or length of the austral winter dry season. Importantly, our lake-based reconstruction of moisture-balance seasonality in equatorial East Africa also helps us understand the oxygen isotope record contained in Mount Kilimanjaro ice. Negative correlation between ice core δ18O and Lake Challa δ18Odiatom implies that moisture balance is not the primary climate control on the long-term trend in ice core δ18O.