Abstract Climate warming is reshaping the surface water system of the world's polar regions. It results in accelerated glacial retreat and melting, lake expansion, and runoff increasing on the Third Pole of the earth (Tibetan Plateau, TP), triggering massive changes in fluvial geomorphology and in the hydrological connections of rivers and lakes. Here we document a reorganization of the endorheic basins (the Zonag Lake and Yanhu Lake basins) in the inner TP, and the establishment of a new hydrological connection with the northernmost source of the Yangtze River, during the period 2011–2019. We find that regional climate change and human actions to mitigate its effects have contributed to this historic hydrological connection, which has been absent for thousands of years. Our findings show that under the influence of global warming and increased precipitation, local hydrological systems will continuously evolve, changing the morphology of rivers and lakes, and affecting the water quantity and quality of the Yangtze River. Given the value of this case in indicating the impact of climate change on the water system in alpine mountains, we suggest the need for global observation and research in other regions with endorheic-exorheic connective basins to gain a more comprehensive understanding and allow better management adaptation.