AbstractLakes developed in the inner depressions of tufa mounds are rare geomorphic features and still poorly understood. Sedimentation in this unusual type of endorheic lake with a very restricted catchment area is highly sensitive to environmental and hydrological changes. The Isona tufa mound complex, north‐eastern Iberian Peninsula, is associated with the discharge zone of a confined artesian aquifer and comprises 11 tufa mounds consisting of an annular rimstone enclosing a central depression filled with lake deposits. Data gathered from trenches excavated in four palaeolakes located within three different morphostratigraphic units permitted a precise analysis of the geometrical characteristics and stratigraphic relationships of the deposits and provided a sedimentation model for the Late Quaternary infilling of the spring‐fed lakes. The work illustrates that trenches allow a precise characterization of the stratigraphic arrangements, lateral facies changes and deformation structures, which are not apparent in studies relying solely on borehole records, and facilitate sampling for dating and geochemical analyses. The five sedimentary facies described represent different evolutionary stages of the lakes, including: (i) carbonate‐rich palustrine deposits probably related to periods with strong hydrological seasonality; (ii) massive highly bioturbated organic ooze; (iii) banded organic carbonate‐rich facies associated with an increase in the regional effective moisture; (iv) fine‐grained quartz‐rich aeolian/slope‐wash sediments; and (v) colluvial facies deposited following the desiccation of the lakes located at higher altitudes. Geochemical and sedimentological analyses of the lacustrine sequences provided information on the palaeohydrological evolution of the Isona tufa mound complex and the palaeoenvironmental conditions of the area over the last 28 ka. Radiometric dating suggests that deposition occurred simultaneously at ca 22 ka in palaeolakes situated at different elevations. A drop in the piezometric level prompted by the opening of springs at lower altitudes probably caused the deactivation of the upper springs and the desiccation of the lakes. Arid conditions prevailed in the area during the Late Glacial and the early Holocene (28·0 to 8·5 ka bp). More humid conditions recorded from 8·5 to 4·2 ka and again since 1·7 ka are in accordance with palaeoenvironmental reconstructions available in the Western Mediterranean since the Last Glacial Maximum.