Though hundreds of caves are known across Mongolia, few have been subject to systematic, interdisciplinary archaeological surveys and excavations to understand Late Pleistocene and Holocene environments. Previous cave excavations in Mongolia have demonstrated their potential for preservation of archaeological and biological material, including Palaeolithic assemblages and Holocene archaeology, particularly burials, with associated organic finds. In other cases, cave surveys found that stratigraphic deposits and archaeological materials are absent. The large number of caves makes the Mongolian Altai Mountain Range a potentially attractive region for human occupation in the Pleistocene and Holocene. Here we present the results of an interdisciplinary survey of caves in four carbonate areas across the Gobi-Altai Mountains. We report 24 new caves, some of which contain archaeological material recovered through survey and test excavations. Most caves presented limited sedimentation, and some were likely too small for human habitation. Six caves showed evidence of palaeontological remains, mostly from likely late Holocene and recent periods. The most notable anthropogenic findings included petroglyphs at Gazar Agui 1 & 13. Gazar Agui 1 also contained lithics and a bronze fragment. Tsakhiryn Agui 1 contained 31 wooden fragments that include an unused fire drilling tool kit and items commonly found in association with medieval burials. We observed that the caves remain in contemporary use for religious and economic purposes, such as the construction of shrines, mining and animal corralling. Water samples from the caves, and nearby rivers, lakes, and springs were analysed for their isotopic compositions (δ18O, δD, δ17O, 17Oexcess, d-excess) and the data, combined with backward trajectory modelling revealed that the Gobi-Altai region receives moisture mainly from western sources. These results form a baseline for future archaeological, paleoclimate and palaeoecological studies about regional seasonality and land use.