The Tibetan Plateau (TP) hosts numerous glaciers and lakes which are critical natural water reserves but highly vulnerable to changing climate. In contrast to general drying trends in global endorheic basins in recent decades, the widespread lake expansions across the endorheic TP stand out as a puzzling “anomaly”. To quantify the contribution of glacier mass changes to lake expansion at fine basin-scale details, we compute spatially resolved estimation of mass change in both glaciers and lakes across the endorheic TP between 2000 and 2010/14 based on multi-mission remote sensing observations. Our glacier mass balance estimates were based on the differences between the newly released global TanDEM-X DEM and the historical SRTM-C DEM, which provide nearly complete coverage (98%) of the glacierized area on the endorheic TP. We provide lake water storage changes of all lakes >1 km2 on the inner TP. These estimates reveal that the massive lake water increase (9.44 ± 1.43 Gt yr−1) was essentially not from the mass loss of glaciers which represents only about 4.7 ± 8.8% of the lake water change (0.44 ± 0.80 Gt yr−1). The relationship in individual basins was, however, highly heterogeneous. About 20% of total lake storage gain had no causality with glacier feeding. In comparison, for 28% of lake water surplus, mainly in the northwestern TP, the positive glacier mass balance infers that glaciers retained some precipitation surplus that could otherwise have been drained to downstream lakes. For the other 52% of lake storage gain, mostly in southern and eastern regions, the glacier mass loss varied among the basins with limited contributing levels (mostly <20%). Our analyses highlight remarkable spatial and temporal variabilities in lake/glacier changes on the endoreic TP and contribute to a better understanding of the role of glaciers in the recent Tibetan lake growth and the impact of climate change on the two types of water reserves.