Groundwater with high nitrate concentrations requires treatment before potable use. Conventional treatment methods such as nanofiltration and reverse osmosis can be used for desalination of most solutes. In contrast, a monovalent selective membrane capacitive deionization (mMCDI) can be used for selective nitrate removal. We use a nanofiltration membrane and anion exchange membranes with an additional neutral layer (AEM-Neutral) or a polyamide layer (AEM-PA) for selective nitrate removal with mMCDI by using a solution of mixed monovalent and polyvalent ions. Monovalent ion selectivity in short-term experiments is up to 17.3 with a nanofiltration membrane, up to 1.7 for AEM-Neutral and up to 5.2 for AEM-PA, whereby the specific energy consumption and water recovery depends on cell structure, applied electric voltage, flow rate and desorption time. Selective nitrate removal with AEM-PA or AEM-Neutral at 0.8 V demonstrated a specific energy consumption of 2 Wh g-1 removed nitrate, lower than pressure-driven membrane processes.