Four distinctive depositional subenvironments of fossil travertines and stromatolites are identified in three high-altitude (3500–4000 m above sea level) lacustrine basins: El Peinado, San Francisco (Las Coladas Salar subbasin), and Las Peladas (southern Andean Altiplano, northwestern Argentina). These late Quaternary occurrences are characterized using geomorphological, sedimentological, petrographic, and stable isotopic data. Stromatolites of cyanobacterial origin only develop in shallow lacustrine margins of El Peinado basin. In the same basin, macrophytic travertines occur both near thermal spring seepage areas along the lake margin as in situ facies and in littoral lacustrine environments up to water depths of several metres as phytoclastic travertine facies. The stromatolites and macrophytic travertines have relatively heavy δ18O compositions, suggesting initial 16O-depleted waters and (or) evaporation effects through time. Their high δ13C compositions are interpreted as a reflection of intense CO2 evasion from the thermal groundwaters feeding the lakes. Similar laminated travertine facies, with no petrographic evidence for biotic origin, occur in both Las Coladas and Las Peladas basins. Neither petrographic nor isotopic data alone can differentiate between these two cases. Besides, diagenetic overprint in Las Peladas facies precludes the use of isotopic values as original isotopic signatures. However, the depositional environmental conditions defined by the geomorphological and sedimentological features are different. Laminated aragonitic crusts in Las Coladas basin formed in a shallow, saline lake and are associated with shoreline and terrace deposits cemented by aragonite. These travertine crusts represent periods of spring, 16O-rich discharge to the lake, as suggested by the lighter oxygen isotopic compositions. In contrast, travertines from Las Peladas occur as laminated calcitic and aragonitic units intercalated at the top of fining-upward sequences composed of conglomerates, sandstones, and intraclastic limestones. Sedimentological data suggest that these travertines originated in fluvial-influenced lake margins during low lake-level episodes.