Laguna Pastos Grandes (Bolivia), nesting in a volcanic caldera, is a large, palustrine-to-lacustrine system fed by meteoric and hydrothermal calco–carbonic fluids. These different fluid inputs favor a complex mosaic of depositional environments, including hydrothermal springs, pools, and an ephemeral lake, producing abundant present-day carbonates developing over a Holocene carbonate crust dated by U–Th. Present-day carbonates (muds, concretions, and microbialites) recorded a large range of isotope variations, reaching 13.9‰ in δ13C and 11.1‰ in δ18O. Sedimentological and geochemical data indicated that the main processes influencing the isotope record were: (i) rapid CO2 degassing and temperature decreases along hydrothermal discharges; (ii) strong evaporation favored by the arid high-altitude Andean climate, locally enhanced by capillary water rise within microbial mats or by wind-induced spray falling on vadose concretions. Unlike past or present perennial lake systems in Central Andes, the short residence time of brine waters in the ephemeral central lake prevents enrichment of lacustrine carbonates in 13C and 18O. The very low fraction modern F14C in these present-day carbonates demonstrates that incorporation of fossil magmatic carbon related to the volcanic context also prevents any radiocarbon dating. The use of isotopes for the interpretation of ancient continental series should always be accompanied by a thorough characterization of the environmental setting.