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Abstract Exceptionally well‐preserved tufas located west of Calama, Atacama Desert, Chile, designated Santa Juana tufas, record episodic wetter conditions, relative to today, over the past 500,000 years. Globally, tufa architecture and depositional details are poorly understood as most described tufas have been degraded by weathering and erosion. In the hyperarid Atacama, post‐depositional alteration is negligible, therefore, the exceptional preservation of Santa Juana tufas documented in this study provides new information about tufa facies and their complex interactions. Santa Juana facies include microbial stromatolites, phytoherms, cascadestone, flowstone and porous limestone. Phytoherms, consisting of former plant stems coated with calcite, developed in channels, within pools, and along spring discharge aprons. Cascadestone, representing former waterfalls, preserves microbial filaments and delicate V‐shaped calcite crystals. Flowstone lines shallow subvertical to subhorizontal channels, representing sites of rapidly sluicing water flow. Porous limestone, containing sparse calcite and/or gypsum and anhydrite cement crystals, represents detrital accumulations. Stable isotope results, coupled with U/Th ages, show that by the Quaternary, relative to the Neogene, groundwater was less supercharged with volcanogenic CO2 so degassing was moderated. The δ18O ratios from Miocene–Pliocene palustrine and lacustrine freshwater carbonates that underlie Santa Juana tufas indicate significant evaporation, but the tufa δ18O signal indicates a less evaporative trend due to shorter atmosphere exposure time. Biological fractionation in δ13C is largely masked by the region's volcanogenic carbon footprint, although tufa petrography shows well‐preserved microbial filaments and laminations. The range of tufa ages in this study shows that there were wetter time periods within the drainage basin headwater area in the Quaternary, but that by the late Pleistocene to early Holocene, aridity to hyperaridity became established. The lack of diagenesis or alteration within the Santa Juana tufas indicates that there has been minimal rainfall since their deposition.