Desert oases are important parts of maintaining ecohydrology. However, irrigation water diverted from the Yellow River carries a large amount of salt into the desert oases in the Hetao plain. It is of the utmost importance to determine the characteristics of water and salt transport. Research was carried out in the Hetao plain of Inner Mongolia. Three methods, i.e., water-table fluctuation (WTF), soil hydrodynamics, and solute dynamics, were combined to build a water and salt balance model to reveal the relationship of water and salt transport in sand dune–wasteland–lake systems. Results showed that groundwater level had a typical seasonal-fluctuation pattern, and the groundwater transport direction in the sand dune–wasteland–lake system changed during different periods. During the crop-growth period (5 May–27 October), the average evapotranspiration values of the sand dune, wasteland–sand dune junction, and wasteland were 31–42% of the reference evapotranspiration. The water consumption of sand dune was 1.95 times that of the wasteland–sand dune junction, and 1.88 times that of wasteland. Water loss of the lake was 761.25–869.05 mm (5 May–27 October). The lake is facing the risk of drying up. The vertical salt transport of groundwater at the sand-dune site was 1.13 times that at the wasteland–sand dune junction site, and 1.82 times that at the wasteland site. Of the groundwater salt of the sand dune, 54% was accumulated in the groundwater of the wasteland–sand dune junction. Of the groundwater salt of the wasteland–sand dune junction, 53% was accumulated in wasteland groundwater, and the remaining 47% was accumulated in the lake. Salt storage of the 1 m soil layer of the sand dune was 85% that of the wasteland–sand dune junction, and 82% that of the wasteland. Research results provide a theoretical basis for the ecohydrology of the Hetao plain.
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