Electrochemical nitrate reduction reaction (NO 3− RR) to ammonia is a promising route to eliminate one of the major pollutants in surface water and groundwater. When powered by renewable electricity, electrolysis provides a sustainable method to generate ammonia from nitrate ions, facilitating the transition from a linear to a circular economy. Optimizing the physical and chemical properties of electrolysis cells is crucial to making this process economically viable for widespread implementation. Here, we explore how the choice of current density, conductivity, pH, interelectrode distance, membrane, catalyst, and buffer solution affect nitrate removal performance and efficiency. We developed a modeling framework to investigate the cell characteristics and fluid dynamics during electrochemical NO 3 − RR using both laminar and bubbly flows. To obtain more precise results, we employed the bubbly flow model (i.e., multiphase fluid) to take into account how gas production near the electrode surface affects liquid velocity, pH distribution, and, ultimately, potential losses. We exploit mass transfer theory to include the current density effect on migration and diffusion. In the absence of a buffer solution, the Nernstian loss became a significant portion of the polarization loss, which increased with current density. We identified the positive effect of the membrane on energy efficiency as being more significant at smaller interelectrode distances. This study provides insights into the origin of potential losses and pH distribution, enabling electrochemical cell optimization for renewable fuel synthesis.