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Abstract Electrochemical nitrate reduction reaction (NO₃RR) has garnered increasing attention as a pathway for converting a harmful pollutant (nitrate) into a value‐added product (ammonia). However, high selectivity toward ammonia (NH₃) is imperative for process viability. Optimizing proton availability near the catalyst is important for achieving selective NH₃production. Here, the aim is to systematically examine the impacts of proton availability on NO₃RR selectivity in a bipolar membrane (BPM)‐based membrane electrode assembly (MEA) system. The BPM generates a proton flux from the membrane toward the catalyst during electrolysis. Thus, the BPM‐MEA system can modulate the proton flux during operation. The impact of interposer layers, proton scavenging electrolytes (CO₃²⁻), and catalyst configurations are also examined to identify which local microenvironments favor ammonia formation. It is found that a moderate proton supply allows for an increase in ammonia yield by 576% when compared to the standard MEA setup. This also results in a high selectivity of 26 (NH₃over NO₂⁻) at an applied current density of 200 mA cm⁻².