Water-splitting electrodialysis (WSED) process using bipolar membranes (BPMs) is attracting attention as an eco-friendly and efficient electro-membrane process that can produce acids and bases from salt solutions. BPMs are a key component of the WSED process and should satisfy the requirements of high water-splitting capability, physicochemical stability, low membrane cost, etc. The water-splitting performance of BPMs can be determined by the catalytic materials introduced at the bipolar junction. Therefore, in this study, several kinds of iron metal compounds (i.e., Fe(OH)3, Fe(OH)3@Fe3O4, Fe(OH)2EDTA, and Fe3O4@ZIF-8) were prepared and the catalytic activities for water-splitting reactions in BPMs were systematically analyzed. In addition, the pore-filling method was applied to fabricate low-cost/high-performance BPMs, and the 50 μm-thick BPMs prepared on the basis of PE porous support showed several times superior toughness compared to Fumatech FBM membrane. Through various electrochemical analyses, it was proven that Fe(OH)2EDTA has the highest catalytic activity for water-splitting reactions and the best physical and electrochemical stabilities among the considered metal compounds. This is the result of stable complex formation between Fe and EDTA ligand, increase in hydrophilicity, and catalytic water-splitting reactions by weak acid and base groups included in EDTA as well as iron hydroxide. It was also confirmed that the hydrophilicity of the catalyst materials introduced to the bipolar junction plays a critical role in the water-splitting reactions of BPM.