Lake Estanya is a small (19 ha), freshwater to brackish, monomictic lake formed by the coalescence of two karstic sinkholes with maximum water depths of 12 and 20 m, located in the Pre-Pyrenean Ranges (North-eastern Spain). The lake is hydrologically closed and the water balance is controlled mostly by groundwater input and evaporation. Three main modern depositional sub-environments can be recognized as: (i) a carbonate-producing ‘littoral platform’; (ii) a steep ‘talus’ dominated by reworking of littoral sediments and mass-wasting processes; and (iii) an ‘offshore, distal area’, seasonally affected by anoxia with fine-grained, clastic sediment deposition. A seismic survey identified up to 15 m thick sedimentary infill comprising: (i) a ‘basal unit’, seismically transparent and restricted to the depocentres of both sub-basins; (ii) an ‘intermediate unit’ characterized by continuous high-amplitude reflections; and (iii) an ‘upper unit’ with strong parallel reflectors. Several mass-wasting deposits occur in both sub-basins. Five sediment cores were analysed using sedimentological, microscopic, geochemical and physical techniques. The chronological model for the sediment sequence is based on 17 accelerator mass spectrometry 14C dates. Five depositional environments were characterized by their respective sedimentary facies associations. The depositional history of Lake Estanya during the last ca 21 kyr comprises five stages: (i) a brackish, shallow, calcite-producing lake during full glacial times (21 to 17·3 kyr bp); (ii) a saline, permanent, relatively deep lake during the late glacial (17·3 to 11·6 kyr bp); (iii) an ephemeral, saline lake and saline mudflat complex during the transition to the Holocene (11·6 to 9·4 kyr bp); (iv) a saline lake with gypsum-rich, laminated facies and abundant microbial mats punctuated by periods of more frequent flooding episodes and clastic-dominated deposition during the Holocene (9·4 to 0·8 kyr bp); and (v) a deep, freshwater to brackish lake with high clastic input during the last 800 years. Climate-driven hydrological fluctuations are the main internal control in the evolution of the lake during the last 21 kyr, affecting water salinity, lake-level changes and water stratification. However, external factors, such as karstic processes, clastic input and the occurrence of mass-flows, are also significant. The facies model defined for Lake Estanya is an essential tool for deciphering the main factors influencing lake deposition and to evaluate the most suitable proxies for lake level, climate and environmental reconstructions, and it is applicable to modern karstic lakes and to ancient lacustrine formations.