High-altitude desert ecosystems exhibit extreme conditions, including intense UV radiation, strong diurnal temperature shifts, and aridity, shaping bacterial abundance and pedogenesis. This study investigates how episodic water availability shapes bacterial abundance and soil forming processes in a temporary lake system on the Barrancas Blancas plain (Ojos del Salado region). Using a multi-method approach, we combined bacterial abundance quantification via extracellular (eDNA) and intracellular (iDNA) DNA, physicochemical soil analyses and ground-penetrating radar surveys to assess subsurface stratigraphy. Meteorological and climatic data further characterized the environmental conditions. Our findings underscore the critical role of episodic water availability in pedogenesis and bacterial abundance. Soil moisture (P1: 31.1%–P2: 11.6%) and electrical conductivity (367–35 µS cm -1 ) decreased with distance from the lake, affecting redox conditions and bacterial biomass. Bacterial abundance peaked in surface soils at intermediate distance from the lake (P4, ∼21 m; iDNA = 1.21 × 10 8 gene copies g -1 soil), consistent with an optimal liquid water availability zone. Proximal sites, despite higher moisture inputs, experience prolonged freezing that delays thaw and limits bacterial abundace, while distal sites lack sufficient meltwater influence. This intermediate zone represents a thermal-hydric equilibrium that maximizes bacterial development. Across all transect positions, iDNA consistently exceeded eDNA (p < 0.001), indicating a predominance of potentially living bacterial biomass throughout the moisture gradient. Stratigraphic analyses revealed sedimentation and erosion cycles, demonstrating the lake’s long-term impact on landscape evolution. This study highlights the significance of high-altitude temporary lakes as natural laboratories for investigating the interactions between bacterial life, pedogenesis, and extreme hydrological regimes. Our results enhance understanding of geo-bio interactions in cryospheric desert environments and have implications for the search of potential life in extraterrestrial analog settings.