Short instrumental streamflow records in the South and East Tibetan Plateau (SETP) limit understanding of the full range and long-term variability in streamflow, which could greatly impact freshwater resources for about one billion people downstream. Here we reconstruct eight centuries (1200−2012 C.E.) of annual streamflow from the Monsoon Asia Drought Atlas in five headwater regions across the SETP. We find two regional patterns, including northern (Yellow, Yangtze, and Lancang-Mekong) and southern (Nu-Salween and Yarlung Zangbo-Brahmaputra) SETP regions showing ten contrasting wet and dry periods, with a dividing line of regional moisture regimes at ~32°−33°N identified. We demonstrate strong temporal nonstationarity in streamflow variability, and reveal much greater high/low mean flow periods in terms of duration and magnitude: mostly pre-instrumental wetter conditions in the Yarlung Zangbo-Brahmaputra and drier conditions in other rivers. By contrast, the frequency of extreme flows during the instrumental periods for the Yangtze, Nu-Salween, and Yarlung Zangbo-Brahmaputra has increased by ~18% relative to the pre-instrumental periods.