Sedimentological and bydrogeological studies are combined in order to investigate the environmental conditions of the lacustrine sedimentation during the Holocene in Gallocanta Lake in Spain. Six units have been identified in the sedimentary succession, based on sedimentological facies and mineralogy, and three depositional stages have been defined: (1) alluvial, (2) carbonate lake system. (3) ephemeral carbonate-saline lake system. The transition between stages 2 and 3 implies a reduction in water inflows to the lake. The delta C-13 isotopical analysis of dolomites points to decaying organic matter as a source of carbon for the dissolved inorganic carbon and evinces that the delta C-13 variations in the lake were probably controlled by organic processes. On the other hand, delta O-18 values could be controlled by modifications in the hydrological system and not necessarily by climatic changes. In this sense, from the hydrological study, three aquifers can be defined: Triassic, Jurassic-Cretaceous and Cenozoic aquifers. The lack of coincidence between the surface and subterranean watershed suggests that the transition between the second and third stages is controlled by a shift of the subterranean watershed. Copyright (c) 2006 John Wiley & Sons, Ltd.