Basin morphology and depositional stratigraphy of Lake Donggi Cona on the north-eastern Tibetan Plateau has been studied with echo depth sounding and shallow seismic sub-bottom profiling. The basin is a pull-apart structure situated at the highly active Kunlun fault. It is characterised by a 92 m deep graben structure in the western part of the lake basin, and a shallow eastern lake part, the latter filled up with fluvial sediments from a large alluvial plain. Three prominent morphological levels were identified at 24 m, 39 m and 57 m below present lake level. They were partly created by basin subsidence, while the deposition of prograding delta sediments primarily formed the morphological steps. The inherited tectonic structures control on-going neotectonic activity, which seems to have only minor influence on present basin morphology. The basin is filled by sediments of at least 30 m thickness in the depocentre. Three major depositional units can be distinguished. In comparison with lithological changes in a sediment core, they give evidence of pronounced lake-level fluctuations and dramatic changes in lake volume. A numerical age datum of ∼19 cal ka BP at the base of the sediment core allows a tentative reconstruction of Late Glacial to Holocene lake development. A very low base level preceded a time of delta formation during higher lake level, i.e. ∼26 m lower than present during Last Glacial Maximum, creating a lake of only 18% of its present size. At the transition to Holocene the lake-level rose very quickly changing to a deep lake environment. Thus, transgression may have promoted maximum lake stands. © 2009 Elsevier Ltd and INQUA.