By using 233 isotope samples, we investigated the spatial and temporal variations of δ(18)O and δ(2)H in precipitation and surface water, and the contribution of different water sources in the rivers within the Tarim River Basin (TRB), which receives snow/glacier meltwater, groundwater, and rainfall. Our study revealed a similar seasonal pattern of precipitation δ(18)O and δ(2)H at both the north and south edges of the basin, indicating the dominant effect of westerly air masses in the summer and the combined influence of westerly and polar air masses during the winter, although the southern part showed more complex precipitation processes in the summer. River water in the basin has relatively large temporal variations in both δ(18)O and δ(2)H showing a distinct seasonal pattern with lower isotope values in May than in September. Higher d-excess values throughout the year in the Aksu river and the Tizinafu river suggest that water may be intensively recycled in the mountains of the TRB. Based on isotopic hydrograph separation, we found that groundwater is the main water source that discharges the entire basin although individual rivers vary.