Rising air temperature, changes in the hydrological cycle and atmospheric circulation patterns are leading to increasing extreme events affecting human and forests worldwide. Altai relict forests are under the risk of degradation under the recent warming. Investigations of climatic impacts on the southern Siberian forest, where temperature is not the main limiting growth factor are still rare and urgently needed. Therefore, we aim to reveal and evaluate the impact of recent extreme climatic events (1919–2019) on relict larch trees (Larix sibirica Ldb.) from two contrasting sites in the Russian Altai (Ersin—HO and Chadan—CH). Application of the state-of-the-art methods of stable isotope and tree-ring analyses is very promising in this region due to high sensitivity of trees to temperature and precipitation changes. We found site-specific differences (ca. 4‰) recorded in newly developed centennial stable carbon (δ¹³C) and oxygen (δ¹⁸O) isotope chronologies, showing their climate sensitivity and reflecting the contrasting conditions at the dry (HO) and wet (CH) sites. The most extreme drought anomalies (σ ≥ + 3σ) over the past 100 years (1919–2019) were revealed for the HO-site in 1935 and 2018. In contrast, a wet extreme anomaly (σ = − 2.7σ) was detected for the CH site only in 1994. Moreover, trees from the CH-site are receiving a greater amount of precipitation during the summer months, especially for the years with extremes σ ≥ − 2σ (1939, 1948, 1958, 1994, 2000, and 2019). Divergent δ¹³C and intrinsic water-use efficiency trends after the 1980s indicate increasing drought stress at the HO- compared to the CH-site, which is confirmed by changes in the running correlation between the isotopes and comparison with declining tree-ring width data. Drought or flooding extremes are recorded heterogeneously at the two study sites in southern Altai, indicating dependence from local habitats, type of soils and freezing active soil depths. Recent climate change affected both forest and humans as public and agricultural sectors are suffering from recent droughts or flooding events. To provide measures and apply mitigation plans for the unique relict forest and public sector, our reconstruction of past anomaly events in this region is important and helpful to predict future climate changes.