We present an alternative radiocarbon (14C) age-depth model using IntCal20 to calibrate new accelerator mass spectrometry (AMS) data applied to a Lake Baikal sediment core (VER99G12) in southern Siberia. 14C dating showed that the core extends to 31 ka. To take into account uncertainties in 14C age and sedimentation depth in the core, a new age-depth modeling routine, undatable, was used in this study. Undatable revealed that significant changes in sedimentation rate correspond to global climate events, either warm or cold, which periods are likely close to the timing of the occurrence of the Meltwater pulses (MWP) at 19 and 14 ka, and the Last glacial Maximum (LGM) at 21–20 ka. Since the Selenga River accounts for 50% of the total river inflow to Lake Baikal, we interpret that these changes in sedimentation rate could be signals of significant changes in Selenga River discharge to the lake, which is expected to be affected by global climate change. Based on pollen analysis, it is highly probable that the sudden influx of the Selenga River to Lake Baikal, particularly at 19 ka, was due to the thawing of permafrost water through the Selenga River, which had developed in the region. Total organic carbon content and mean grain size increases concurrent with sedimentation rate, suggesting river inflow increased available nutrients for biological activity. Our results indicate that hydrological changes corresponding to MWP events can be observed in continental areas of the Northern Hemisphere.