Nitrate is a toxic yet valuable ionic species, and nitrate capture from low-concentration streams presents an opportunity for resource recovery and a research challenge. Building on our previous study on nitrate concentrating at moderate concentration (7 mM), this study focused on even lower nitrate concentration down to 0.5 mM by advancing the electrodialysis system with tailored membrane choices and careful electrodialysis design aiming for efficient KNO3 concentrating. First, comprehensive study was conducted on the counter-ion diffusion across nine commercial AEMs and CEMs, revealing distinctive diffusion behavior across different types of membranes, pinpointing FAS−PET−130 and FKL−PK−130 as the optimal pair in constructing ED cell for nitrate electrodialysis due to low counter-ion diffusion. Based on the counter-ion diffusion slope, the maximum concentrating ratio (Cc/Cs) of 126 for the membrane combination. With a safe design margin, a maximum ratio of 100 for Cc/Cs was adopted in the following electrodialysis study. Theoretical pair voltages were accounted for Donnan and Ohmic contributions between experimental observations and theoretical prediction. The source solution and concentrate solution were explored to ensure high coulombic efficiency under various pair voltages. In particular, with an ultralow source concentration of 0.5 mM (i.e., 7 ppm nitrate-N), the successful nitrate concentrating was demonstrated with 50 mM of concentrate solution at 0.1 mA/cm2, with 96%−98% of coulombic efficiency. A low level of pair volage of −0.27 V at beginning to −0.85 V after 1,930 s was observed, which are close with theoretical predictions (−0.29 V to −0.70 V), confirming the highly efficient nitrate concentrating. These results demonstrate the feasibility of selective ion recovery from dilute streams and support future work on system durability and scale-up.