By collecting the atmospheric precipitation, surface water, and groundwater in the Inner Mongolia section of the Yellow River Basin in July 2021 (wet season), October (normal season), and April 2022 (dry season), stable isotope technology was used to analyze the temporal and spatial changes in hydrogen and oxygen stable isotopes in the "three rivers" of the basin, and the MixSIAR mixing model was used to reveal the water body transformation relationship. The results showed that the mean difference in the groundwater isotope was small in the abundance period, flat period, and dry period in the Mongolia section of the Yellow River Basin. The groundwater regeneration was slow, the retention time was long, the seasonal variation was not obvious, and the δD value of surface water was higher in the abundance period than in the normal period and dry period. According to the δ18O and δD diagrams, the slope and intercept of surface water lines in the three periods were smaller than those of local precipitation lines, and surface water was affected by evaporative fractionation after receiving precipitation recharge. The δD values of surface water on the north bank of the Yellow River showed a trend of first increasing and then decreasing from upstream to downstream, while the δD values of surface water on the south bank of the Yellow River showed a trend of gradually decreasing from upstream to downstream. The recharge contribution of groundwater in surface water in the high-water period accounted for 2.9%, precipitation accounted for 97.1%, surface water accounted for 5.0%, atmospheric precipitation accounted for 95.0%, surface water accounted for 56.6%, and precipitation accounted for 43.4%, and the recharge contributions of precipitation and surface water to groundwater in the high water period were 47.6% and 52.4%, respectively. Those in the normal period were 30.7% and 69.3%, and those in the dry period were 37.8% and 62.2%, respectively. Atmospheric precipitation was the main replenishment source of surface water, showing that the replenishment ratio in the wet season was larger than that in the normal season and dry season, which was closely related to the total precipitation and its distribution in each period. Surface water was the main replenishment source of groundwater, showing that dry season > normal season > wet season.
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