Electrochemical nitrate reduction reaction (NO3 -RR) to ammonia is a promising route to eliminate one of the major pollutants in surface 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 make this process economically viable for widespread implementation. Here, we explore how the choice of current density, conductivity, pH, inter-electrode distance, membrane, catalyst, and buffer solution affect nitrate removal performance and efficiency. We develop a modeling framework to investigate the cell characteristics and fluid dynamics during electrochemical NO3-RR using both laminar and bubbly flows. To obtain more precise results, we employed the bubbly flow model (i.e., Multi-phase 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 to be more significant at smaller inter-electrode distances. This study provides insights into the origin of potential losses and pH distribution, enabling electrochemical cell optimization for renewable fuel synthesis. Next, we will discuss our recent work on designing single atom alloys (SAAs) for selective conversion of low concentration nitrate ions in natural wastewater streams from Dairy farm into ammonia. We benchmarked the catalyst's selectivity, activity, and stability following standard protocols established in the field of nitrogen fixation, including control experiments by using an electrolyte that does not contain nitrate ions and performing experiments under the same operating conditions using nitrogen isotopes (i.e., 14NO3 -, 15NO3 -).