Soil water deficit and saline-alkaline stress impose severe constrains to agriculture and vary across different salt-tolerant crops. Yet, the effects and mechanisms of plant salt tolerance on long-term soil water budget and future root zone (both primary and secondary) salinization and alkalization trends under changing environments in irrigated agroecosystems have not been fully understood, particularly driven by seasonal irrigation practices and stochastic climate conditions. Here, we introduce a robust species-dependent soil water, salinity, and sodicity coupled model that enables explicitly simulation to the feedback between evapotranspiration and salinity being shaped by plant salt tolerance and saturated hydraulic conductivity as affected by salinization and alkalization in seasonally irrigated agroecosystems. Using this model in conjunction with field comprehensive measurements from a typical arid inland river basin in Northwest China, we find that the species-dependent model performed well in simulating the root zone moisture (s), salinity (Cs) and sodicity (Ex) dynamics as driven by seasonal irrigation and random precipitation under different salt-tolerant crops, with average consistency measure (CM) reaching to 0.825 ± 0.017, 0.819 ± 0.027 and 0.728 ± 0.033, respectively. Stochastic simulations indicate that plant salt tolerance plays a predominant role in regulating the feedback of vegetation on soil water budget and root zone salinity and sodicity levels over time in seasonally irrigated agroecosystems. In contrast to salt-sensitive species, salt-tolerant plants seems to exhibit higher efficiency in water extraction from soil, with higher evapotranspiration rates, less frequent leaching events and greater capillary upflow fluxes, thereby lowering soil moisture and boosting salinization and alkalization in the root zone, particularly in arid climates. Sensitivity analysis revealed that plant salt tolerance, together with climatic forcing and anthropogenic perturbations, can significantly modulate the soil water balance and determine the possible trends of root zone salinization and alkalization in future, thus controlling potential risks of soil degradation related to reducing soil hydraulic conductivity Ks(Cs, Ex) in irrigated agroecosystems. Notably, since Ks(Cs, Ex) decreases with plant salt tolerance increases, salt-resilient species have the potential to exacerbate soil degradation. Our results emphasize the importance of comprehensively considering plant salt tolerance for assessing the sustainability of agricultural management practices and environmental protection measures, as well as proposing adaptive strategies under global changes.