Oxygen isotopes of diatom silica and petrographical characterisation of diatomaceous laminated sediments of Lago Chungará (northern Chilean Altiplano) have allowed us to establish its palaeohydrological evolution during the Lateglacial–early Holocene (ca. 12 000–9400 cal. yr BP). These laminated sediments are composed of light and dark pluriannual couplets of diatomaceous ooze formed by different processes. Light sediment laminae accumulated during short-term diatom blooms whereas dark sediment laminae represent the baseline limnological conditions during several years of deposition. Oxygen isotope analysis of the dark diatom laminae show a general δ18O enrichment trend during the studied period. Comparison of these δ18Odiatom values with the previously published lake-level evolution suggests a correlation between δ18Odiatom and the precipitation:evaporation ratio, but also with the evolution of other local hydrological factors as changes in the groundwater outflow as well as shifts in the surface:volume ratio of Lago Chungará. The lake expanded (probably increasing this ratio) during the rising lake-level trend due to changes in its morphology, enhancing evaporation. Furthermore, the lake's hydrology was probably modified as the groundwater outflow became sealed by sediments, increasing lake water residence time and potential evaporation. Both factors could cause isotope enrichment. © Natural Environment Research Council (NERC) copyright 2008. Reproduced with the permission of NERC. Published by John Wiley & Sons, Ltd.