Concerns have been raised about the negative impacts of global warming on the hydrological climate change and ecosystems of Asia. Research on the high-altitude mountainous regions of Asia with relatively short meteorological and hydrological records relies on paleoclimate proxy data with long time scales. The stable isotopes of tree-rings are insightful agents that provide information on pre-instrumental climatic and hydrological fluctuations, yet the variability of these data from different regions along the Tianshan Mountains has not been fully explored. Herein, we related climate data with tree-ring width (TRW) chronologies and δ13 C (stable carbon isotope discrimination) series to discern if the Picea schrenkiana in the Ili and Manas River Basins are sensitive to climatic factors and baseflow (BF). The results show significant correlations between temperature and TRW chronologies, temperature and δ13 C, relative humidity and TRW chronologies, and BF and δ13 C. Temperature, particularly the mean late summer to early winter temperature, is a pronounced limiting factor for the tree-ring and the δ13 C series in the Manas River Basin, located in the middle of the North Tianshan Mountains. Meanwhile, mean early spring to early autumn temperature is a limiting factor for that of the Ili River Basin, located on the southern slope of the North Tianshan Mountains. We conclude that different seasonal variations in temperature and precipitation of the two river basins exerted significant control on tree growth dynamics. Tree-ring width and tree-ring δ13 C differ in their sensitivity to climate and hydrological parameters to which tree-ring δ13 C is more sensitive. δ13 C showed significant lag with precipitation, and the lag correlation showed that BF, temperature, and precipitation were the most affected factors that are often associated with source water environments. δ13 C series correlated positively to winter precipitation, suggesting baseflow was controlling the length of the growing season. The tree-ring δ13 C provided information that coincided with TRW chronologies, and supplied some indications that were different from TRW chronologies. The carbon stable isotopes of tree-rings have proven to be powerful evidence of climatic signals and source water variations. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.