The Root Zone Water Quality Model (RZWQM) is a one-dimensional process-based model used for simulating major physical, chemical, and biological processes in agricultural systems. To date, the model has not been applied to potato production systems for simulating nitrate leaching. In this study, 35 datasets collected between 2009 and 2016 at a field under a three-year potato (potato–barley–red clover) rotation in Prince Edward Island (PEI), Canada, have been employed for calibrating and validating the water, nitrogen (N) cycling, and plant growth routines of RZWQM and for subsequently estimating nitrate leaching. The model fitness, evaluated using univariate and bivariate indicators, was rated as high for most of the parameters tested. As a result of the combined influence of higher infiltration and reduced plant uptake, the model showed that the highest leaching at the rotation level occurred between September and December. A secondary leaching period occurred in spring, when residual soil nitrate was mobilized by increased percolation due to snowmelt. Most of the nitrate leaching occurred during the potato year (89.9 kg NO₃–N ha⁻¹ y⁻¹), while leaching for barley and red clover years had comparable values (28.6 and 29.7 kg NO₃–N ha⁻¹ y⁻¹, respectively). The low N use efficiency of the entire rotation (i.e., 30.2%), combined with the high NO₃–N concentration in leachate (i.e., 34.9 mg NO₃–N L⁻¹ for potato and 16.3 mg NO₃–N L⁻¹ for the complete rotation), suggest that significant efforts are required for adapting management practices to ensure sustainability of potato production systems.