Nitrate is among the important types of pollutant sources in drinking water worldwide, and there are a number of methods to remove it from water. New treatment methods are being developed as an alternative to traditional treatment methods. One of them is membrane capacitive deionization (MCDI). In this study, the removal of nitrate ions with MCDI system was investigated. Nitrate solutions were treated via MCDI at different operating conditions. The obtained nitrate removal efficiency reached 83.07% at a flow rate of 2.5 L/min and a potential of 0.8 V was applied. In addition, during the nitrate removal of the MCDI system, the environmental effects were evaluated by life cycle analysis. As a result of these analyses, MCDI system offered advantages of low energy demand and low-energy environmental effects during operation. The results showed that the improved MCDI technology holds a great potential to be an energy-efficient process for nitrate removal. Life cycle assessment was applied to the experimental study. According to the assessment, water consumption had the highest effect in all damage assessment categories.