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The protection of an unsaturated zone is essential for groundwater-quality security. Neglecting pollutant changes in the saturated zone can affect the accuracy of groundwater-quality assessments. Unlike water sampling, the nonreproducibility of soil sampling complicates the observation of contaminant changes at different times in the same location. The HYDRUS-2D model, coupled with the Richards equation and the convection-dispersion equation, was applied to simulate the migration and transformation of high ammonia concentrations in wastewater in an unsaturated zone. Long-term field observations were carried out for trinitrogen (NH4+, NO2-, and NO3-) from 2015 to 2018 at a wastewater discharge site located in a desert area in northwest China. Samples were collected twice a month. The model was calibrated and validated using statistics and observation data. Variations in trinitrogen concentrations were simulated using the model and fitted well with the measured values. Simulation results for trinitrogen migration and transformation demonstrated that there was no enrichment on the ground surface. Contaminants attenuated rapidly in the unsaturated zone after wastewater discharge stopped. NH4+ was oxidized to NO2 and NO3- under nitrification, except in the anoxic subclay lenses. Subclay lenses were not considered in previous research. These lenses had high enrichment with contaminants and prevented secondary nitrification, which might have led to extremely low NO3- concentrations. The removal rate of contaminants by the unsaturated zone in natural conditions is as high as 76%, and contaminants could be degraded to acceptable levels within 10 years (3650 days) without artificial interventions. This indicates that the unsaturated zone can delay migration and degrade contaminants, and should be taken into consideration in groundwater-quality assessments.