With the implementation of water-conservation projects in the Hetao Irrigation District (HID), great changes have taken place in the ecohydrological process. A cultivated land–wasteland–lake system in the upper Yellow River Basin (YRB) was chosen to study the soil salt and water transport process with the Hydrus-1D model. The model parameters were calibrated and validated by measuring the soil salt and water data. Measured values were in good agreement with the simulated values. The results showed, in the whole growth period, the deep percolation of cultivated land was 34–40% of the total applied water (rainfall and irrigation). The capillary rise in the cultivated land, wasteland, and lake boundary was 24%, 29–35%, and 62–68% of their own evapotranspiration, respectively. The capillary rise in the lake boundary was about 2 times that of the wasteland and 2.6 times that of the cultivated land. The salt storage in the 1 m soil zone of the lake boundary was more than 10% and 18% greater than that of the wasteland and cultivated land, respectively. The salt of the capillary rise in the lake boundary exceeded that of the wasteland by a factor of three. The salt accumulation in the upper soil zone of the cultivated land, wasteland, and lake boundary was 13%, 37%, and 48%. Soil salinization in the upper soil zone of the wasteland and lake boundary was serious, and some measures should be taken to reduce the salt content to prevent soil salinization. The results act as a theoretical basis for the ecohydrological control of the HID.

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