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We investigate the Holocene sedimentary infilling of two high-altitude (>4000 m a.s.l.) lacustrine basins in the subtropical regions of the Atacama Altiplano (Central Andes, northern Chile) that today contain permanent, shallow saline lakes: Laguna del Negro Francisco (27 degrees S) and Laguna Miscanti (23 degrees S). Laguna Miscanti was surveyed with multi-frequency, high-resolution seismic techniques and sediment cores were retrieved from offshore areas of both lakes. Because of the geological location of these lacustrine basins within the active Andean convergent margin, and the presence of present and past climatic gradients in the Altiplano, our detailed sedimentologic, mineralogic and geochemical study evaluates tectonic, volcanic, and climatic controls on lacustrine sedimentation in an arid environment. Both lakes originated by tectonic and volcanic activity during the Pleistocene. Tectonic control of basin dynamics was clearly exerted during the early stages: increased subsidence was responsible for alluvial fan activity in the Laguna Miscanti Basin prior to the establishment of the lake, and the Negro Francisco Basin changed from exorheic to endorheic. Hydrogeologic conditions needed to maintain the two perennial saline lakes are largely controlled by the basins’ tectonic history. The evolution of Laguna del Negro Francisco comprises four successive stages: (1) perennial saline carbonate-sulfate lake; (2) saline pan-saline lake complex with a carbonate-sulfate brine; (3) a perennial brackish stage with high macrophyte (Chara) productivity and mostly calcite formation; and (4) a residual stage with halite precipitation. The depositional history recorded in the Miscanti core illustrates the evolution from an aragonite-producing, ephemeral saline lake to a macrophyte-dominated perennial brackish lake, with an aragonite saline pan-saline lake complex and a calcite-producing perennial brackish lake as intermediate stages. The hydrologic budget of the lakes is a direct response to effective moisture (precipitation-evaporation) fluctuations and, therefore, climate variability has played a major role in chemical composition and lake level changes. Climate forcing has controlled the depositional history of the lakes during the Holocene. Our study illustrates different responses of lake systems to external climatic forcing, especially with respect to cyclicity, threshold dynamics and the importance of sedimentary recycling. The main sedimentary sequences in both lakes correspond to cycles of increasing and decreasing effective moisture. However, this cyclicity is characterized by abrupt change rather than gradual evolution. Threshold dynamics modulated limnogeological changes and caused a stepwise evolution of the lacustrine systems. Laguna Miscanti and Laguna del Negro Francisco sedimentary sequences provide depositional models for small, topographically closed, brackish to saline lakes that developed on active margins and evolved under fluctuating but generally arid climatic conditions. (C) 1999 Elsevier Science B.V. All rights reserved.