Many lake basins on the Tibetan Plateau are affected by tectonic activity. It is therefore important to consider seismotectonic influence on lake evolution when discussing climate impact on hydrology and sediment budgets. Lake Donggi Cona serves as an example to demonstrate the influence of the Kunlun left-lateral strike-slip fault on lake formation with subsidence in the pull-apart basin. The results show that comparable fluvial sandy sediments generated at low lake levels during the Late Glacial and early Holocene occur at different water depths within a double lake-internal pull-apart structure, suggesting mean subsidence rates of 2.6–4.3 mm/a since 13.5 cal. ka BP. Such pulses prevailed throughout the Holocene, pointing to repeated seismic events and ongoing neotectonic activity. Sediment distribution and changing morphological shape by subsidence are important factors that affected other lakes on the Tibetan Plateau and enable us to distinguish between neotectonic and paleoclimatic impacts.