Notwithstanding its crucial importance for assessing the vulnerability of tropical mountain ecosystems to both local anthropogenic pressure and climate change, knowledge of the relationships between climate, hydrology, and vegetation on Mount Kilimanjaro is highly fragmentary. Unraveling the pathway of water from precipitation to transpiration can also help validate paleoclimate proxies derived from the hydrogen‐ and oxygen‐isotopic signatures of plant compounds, such as leaf waxes. We measured δ2H and δ18O in precipitation, stream, and soil water, and in xylem and leaf water of locally common plants, for four successive seasons along a 3,000‐m altitudinal transect covering lowland savannah, lower and upper montane forest, and the subalpine zone on Mount Kilimanjaro. Across all four bioclimatic zones, δ2H and δ18O in precipitation decreased with monthly precipitation amount at a rate of −8 ± 2‰ and −1.0 ± 0.3‰ per 100 mm, respectively. Our xylem‐water isotope data indicate that plants in general took up topsoil water during the northeasterly monsoon season and short dry season and gradually shifted to deeper soil water during the southeasterly monsoon season and the main dry season. Savannah trees and shrubs tapped from a water pool recharged by source water with a relatively constant isotopic signature. This observation conforms to the “two water worlds” hypothesis and implies a possible seasonal bias in plant‐derived paleohydrological proxies. Finally, our results show strong correlation between xylem‐to‐leaf water‐isotopic enrichment and ambient relative humidity, despite a bias in the savannah that we attribute to a leaf‐cooling mechanism in this warm, semi‐arid environment.