Speleothems from caves in near-permafrost regions can provide unique insights into the climatic history of temperature-sensitive environments. These regions are often remote and only seasonally accessible, which makes cave monitoring – a requirement for speleothem-based proxy interpretation – challenging. We document ventilation, the infiltration regime, and the isotopic composition of dripwater in Botovskaya Cave in southern Siberia, a host to speleothems previously used to reconstruct Quaternary permafrost dynamics in continental Eurasia. We explore surface and cave temperature records, cave air CO2 concentration data and stable isotopes in precipitation and dripwater and evaluate infiltration conditions and the sensitivity of speleothems to regional atmospheric dynamics. Locations further into the cave are thermally more stable (T = 1.8 – 2.5 ± 0.1°C) than sites closer to the entrances which show inter-seasonal temperature variability of ca. 4°C. Cave CO2 concentration is highest during summer when the cave acts like a cold trap and cave air becomes stagnant and in winter when frozen ground and epikarst and entrances closed by snow subdue ventilation. Accordingly, sub-horizontal Botovskaya Cave ventilates via vertical joints and the entrances during spring whenever cave air is warmer than the surface air. Dripwater isotopic composition (δ18O and δ2H) generally reflects the mean isotopic composition of precipitation, but δ18O decreases with distance from the entrances, and in the deeper sections of the cave reflects the mean (multi)annual isotopic composition in precipitation, likely due to an increasing contribution of snowmelt to total infiltration. Slope aspect and vegetation density above the cave section determine the proportion of received seasonal precipitation. On local scale our results provide insights into the environmental processes that govern the microclimate in Botovskaya Cave and facilitate robust interpretation of future speleothem-based proxy reconstructions. On the pan-regional scale we propose a potential mechanism responsible for suboptimal reproducibility of stalagmite records from the same cave.