At the beginning of this century, some new lakes unexpectedly appeared in the Taklamakan Desert – one of the largest and driest deserts in the world. The origin of the water in the new lakes, however, has been a matter of debate. We test the hypotheses by analyzing water samples collected from the new lakes, the Bosten Lake and the foothills of the mountains that surround the desert. Using the isotopic composition of these waters as tracers, together with data from remote sensing, local weather stations and stream gauges, we infer that the new lakes may originate from increased recharge of groundwater from meltwater in the nearby mountains. We further speculate, supported by first‐order simulation of earthquake‐induced discharge of groundwater from mountains, that the source of this increased recharge may be related to earthquake‐induced discharge of groundwater from nearby Altyn and Kunlun Mountains.