Lake Chungará (18°15′S, 69°09′W, 4520 m above sea-level) is the largest (22·5 km2) and deepest (40 m) lacustrine ecosystem in the Chilean Altiplano and its location in an active volcanic setting, provides an opportunity to evaluate environmental (volcanic vs. climatic) controls on lacustrine sedimentation. The Late Quaternary depositional history of the lake is reconstructed by means of a multiproxy study of 15 Kullenberg cores and seismic data. The chronological framework is supported by 10 14C AMS dates and one 230Th/234U dates. Lake Chungará was formed prior to 12·8 cal kyr bp as a result of the partial collapse of the Parinacota volcano that impounded the Lauca river. The sedimentary architecture of the lacustrine succession has been controlled by (i) the strong inherited palaeo-relief and (ii) changes in the accommodation space, caused by lake-level fluctuations and tectonic subsidence. The first factor determined the location of the depocentre in the NW of the central plain. The second factor caused the area of deposition to extend towards the eastern and southern basin margins with accumulation of high-stand sediments on the elevated marginal platforms. Synsedimentary normal faulting also increased accommodation and increased the rate of sedimentation in the northern part of the basin. Six sedimentary units were identified and correlated in the basin mainly using tephra keybeds. Unit 1 (Late Pleistocene–Early Holocene) is made up of laminated diatomite with some carbonate-rich (calcite and aragonite) laminae. Unit 2 (Mid-Holocene–Recent) is composed of massive to bedded diatomite with abundant tephra (lapilli and ash) layers. Some carbonate-rich layers (calcite and aragonite) occur. Unit 3 consists of macrophyte-rich diatomite deposited in nearshore environments. Unit 4 is composed of littoral sediments dominated by alternating charophyte-rich and other aquatic macrophyte-rich facies. Littoral carbonate productivity peaked when suitable shallow platforms were available for charophyte colonization. Clastic deposits in the lake are restricted to lake margins (Units 5 and 6). Diatom productivity peaked during a lowstand period (Unit 1 and subunit 2a), and was probably favoured by photic conditions affecting larger areas of the lake bottom. Offshore carbonate precipitation reached its maximum during the Early to Mid-Holocene (ca 7·8 and 6·4 cal kyr bp). This may have been favoured by increases in lake solute concentrations resulting from evaporation and calcium input because of the compositional changes in pyroclastic supply. Diatom and pollen data from offshore cores suggest a number of lake-level fluctuations: a Late Pleistocene deepening episode (ca 12·6 cal kyr BP), four shallowing episodes during the Early to Mid-Holocene (ca 10·5, 9·8, 7·8 and 6·7 cal kyr BP) and higher lake levels since the Mid-Holocene (ca 5·7 cal kyr BP) until the present. Explosive activity at Parinacota volcano was very limited between c. >12·8 and 7·8 cal kyr bp. Mafic-rich explosive eruptions from the Ajata satellite cones increased after ca 5·7 cal kyr bp until the present.