This study aims to address the harmful effects of excessive nitrogen fertilizer by investigating the mobility-retardance effect of zeolite on nitrate movement in loam soil columns. Disturbed and undisturbed soil columns, treated with zeolite as well as control soil columns, were analysed over a span of three years. Breakthrough curves generated from the experiments were evaluated using the HYDRUS-1D code with mobile–immobile water (MIM) and dual-permeability (DP) models. Our findings highlight that zeolite application significantly reduced nitrate mobility, with recovery rates decreasing by 8% in disturbed and 11% in undisturbed columns. The DP model, which accurately reflects real soil water flow conditions, outperformed the MIM model in predictive accuracy. This research offers a novel long-term perspective on the benefits of zeolite in enhancing soil properties and mitigating nitrate leaching, recommending the DP model for superior prediction of contaminant transport in structured soils within the vadose zone.