To study the transformation of surface water and groundwater and during irrigation and the migration law of salts in the Hetao Irrigation District, Wuyuan County of Bayannur City in the irrigation district was taken as the research object. Isotope tracer, hydrochemical analysis method, and linear end-element mixed model were used to quantitatively evaluate the conversion amount of channeled water, groundwater, and stagnant water in the land. The results show that the proportion of the channeled water and the groundwater recharge to stagnant water in the land is 65.15% and 34.85%, respectively. The salt recharge of the channeled water and the groundwater to the stagnant water in the land accounts for 53.31% and 28.52% of the total salt of the two sources, respectively, and 18.17% of the salt remains in the irrigation district during the process of recharge to the stagnant water in the land.