Significant air temperature and precipitation changes have occurred since the 2000s in vulnerable Siberian subarctic regions and urged updates of available chronologies towards the third millennium. It is important to better understand recent climatic changes compared to the past decades, centuries and even millennia. In this study, we present the first annually resolved triple tree-ring isotope dataset (δ¹³C, δ¹⁸O and δ²H) for the eastern part of the Taimyr Peninsula (TAY) and northeastern Yakutia (YAK) from 1900 to 2021. We found that the novel and largely unexplored δ²H of larch tree-ring cellulose was linked significantly with δ¹⁸O for the YAK site, which was affected by averaged April–June air temperatures and evaporation. Simulated by the Land Surface Processes and Exchanges (LPX-Bern 1.0) model, the water fraction per year for soil depths at 0-20 and 20-30 cm was significantly linked with the new eco-hydrological tree-ring δ²H data. Our results suggest increasing evapotranspiration and response of trees’ water relation to rising thaw water uptake from lower (20–30 cm) soil depth. A positive effect of July air temperature on tree-ring δ¹⁸O and a negative impact of July precipitation were found, indicating dry conditions. The δ¹³C in larch tree-ring cellulose for both sites showed negative correlations with July precipitation and relative humidity, confirming dry environmental conditions towards the third millennium.