Drip irrigation with alternate use of fresh and brackish waters is an excellent irrigation strategy to overcome salt stress problems induced by brackish water. Understanding salt stresses in the soil profile and their relationship with crop growth is critical when optimizing irrigation strategies with alternate use of fresh and brackish waters. The HYDRUS (2D/3D) model was calibrated and validated using experimental data collected in 2019 and 2020, respectively. The calibrated model was then used to evaluate the effects of different irrigation strategies involving the use of only freshwater (FW) or brackish water (BW), or the alternative use of brackish and fresh waters (1B1F, one irrigation with brackish water and one with fresh water; 2B1F, two irrigations with brackish water and one with fresh water; and 3B1F, three irrigations with brackish water and one with fresh water) on the soil electrical conductivity (ECsw), salt stress, crop growth, and yield. In general, the model performed well, with the average RMSE, M RE , and R2 for ECsw of 0.12 dS m−1, 6.85%, and 0.97, respectively. The average ECsw in the 0–40 cm soil layer (the main root zone) showed large differences between different alternate irrigation strategies, increasing by 55.9% between FW and BW. There was a strong linear relationship between salt stress (ECsw of 3.4–11.8 dS m−1, SS) in the main corn root zone and salts introduced by irrigation water. The SS duration and area increased with the frequency of irrigations with brackish water, while the opposite was observed for the average desalination rate (DR) after irrigation during the entire growth stage. The SS duration was 90, 111, 115, 121, and 121 days for FW, 1B1F, 2B1F, 3B1F, and BW, respectively, while the corresponding values for the duration of high salt stress (ECsw of 7.6–11.8 dS m−1, HSS) were 4, 24, 32, 37, and 46 days, respectively, and the average DRs were 4.3%, 2.4%, 1.9%, 1.7%, and 0.8%, respectively. Average fractions of the SS and HSS areas to the main root zone area for BW increased by 5.3% and 26.6% compared with FW, respectively. When the HSS duration increased by 42 days from the FW to BW scenarios, corn yield, plant height, stem diameter, and leaf area index decreased by 8.8%, 10.4%, 17.7%, and 19.6%, respectively. Additionally, the quantitative relationship between SS and corn yield, i.e., a sensitivity function of the crop yield to soil water and salt stresses, was proposed based on HYDRUS (2D/3D) simulations. The 2B1F scenario can be recommended as the optimal strategy for the studied region, using most brackish water with only a 4% decrease in the corn yield.
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