This study enhances nitrate recovery from groundwater using a hybrid membrane process, combining electrodialysis (ED) and nanofiltration (NF) with response surface methodology (RSM). Employing the Box–Behnken design (BBD), the research explored key operational factors affecting nitrate removal. A quadratic model demonstrated strong predictive accuracy, with an R2 close to 1 and errors below 5% for responses such as nitrate content, specific energy consumption (SEC), and water recovery (Y%). While a single NF system achieved less than 60% nitrate removal, combining it with ED resulted in a total nitrate removal rate of up to 91%, a recovery rate of 75.25%, a lower SEC of 1.25 kWh/m³, and a nitrate level of 46.10 mg/L, producing water that meets drinking water standards, but which is slightly corrosive yet non-scaling.