Recent studies using environmental isotopes (²H, ³H, ¹⁴C, ¹⁸O, and ²²²Rn) were summarized to trace hydrological processes in the Heihe River Basin (HRB). Isotopic values from various types of waters (i.e., precipitation, surface water, and groundwater) at multiple spatiotemporal scales within the basin have been synthesized. The measurements of δD and δ¹⁸O values show that: precipitation in the upper-basin constitutes the primary source for surface water and shallow groundwater in the HRB; frequent surface water-shallow groundwater exchanges take place mainly in the middle HRB; and in the lower HRB, shallow groundwater is recharged primarily by river water while deep groundwater is largely isolated from modern recharge sources. This finding for the lower HRB is further confirmed by ¹⁴C and ³H measurements, which demonstrate that shallow, unconfined groundwater is younger than deep, confined groundwater. Future research should be focused more on increasing sampling resolution in time and space, utilizing multiple isotopes in tandem with other geochemical tracers for more quantitative research, as well as integrating results from isotope-based, geochemical investigations into construction and calibration of numerical models.