Bipolar membrane electrodialysis (BMED) has emerged as a promising technology for integrating saline water treatment with CO2 capture systems. However, a significant challenge remains in the form of proton leakage, which depletes the OH− ions generated by the bipolar membrane (BPM), thereby directly hindering CO2 absorption efficiency. To unravel the underlying mechanism of proton leakage and optimize BMED performance, a continuous feed-bleed BMED system for both saline water treatment and CO2 capture was proposed. A comprehensive investigation was conducted to assess the influence of key parameters, including current density, alkalinity ion concentration, feedstock salinity, and product concentration on the extent of H+ leakage. Notably, it’s found that increasing current density from 150 to 300 A/m2, the proportion of H+ leakage through the anion exchange membrane (AEM) rose from 65.53 % to 74.77 %, while alkalinity ion concentration has a relatively minor impact. To manage the feedstock salinity and product concentration, the NaCl and H2O feeding rates were precisely regulated in this feed-bleed system. By adjusting these rates to 8–15 mL/min for NaCl and 3–8 mL/min for H2O, respectively, a notable reduction in the H+ leakage rate was achieved, from 71.37 % down to 57.97 %. Furthermore, through the integration of iterative calculations with experimental data, it was discovered that proton leakage predominantly occurs via concentration diffusion mechanisms. This insight into the intricate regulation of proton leakage not only deepens our understanding of the underlying mechanism but also provides valuable guidance for the effective deployment and optimization of BMED technology.