Hydrogen production via water electrolysis using desalinated seawater offers a sustainable energy solution and has attracted considerable attention in recent years. However, its efficiency depends heavily on the quality of water. Many studies have not explored the relationship between treated water quality and hydrogen generation efficiency at each stage of the seawater desalination process. This study examines a three-step seawater desalination process comprising softening with ballasted flocculation (SBF) as a pretreatment, reverse osmosis (RO) as the main desalination step, and ion exchange as a polishing step to provide high-quality water for electrolysis. Water from each purification stage was supplied to the electrolyzer to compare the impact on water quality and hydrogen generation efficiency. The SBF process removed magnesium (Mg) and calcium (Ca) from seawater, as well as turbidity and bacteria, but hydrogen production via water electrolysis continued for no more than 10 h. However, when feeding RO water and RO water processed by ion exchange after the SBF process, hydrogen was generated stably and continuously for 70 h, achieving high efficiency comparable to that of commercial pure water. High production of green hydrogen by water electrolysis is possible through RO seawater desalination combined with SBF pretreatment.