A seawater desalination system includes an intake part buried in a sand layer of the seafloor to take in seawater passed through the sand layer, an anterior filtration part filtering seawater conveyed from the intake part, and a posterior filtration part filtering seawater conveyed from the anterior filtration part, using a reverse osmosis membrane. The anterior filtration part includes a first anterior filtration line including a first ultrafiltration membrane, a second anterior filtration line including a second ultrafiltration membrane having a molecular weight cut-off less than that of the first ultrafiltration membrane, and a switching part switching a path through which seawater flows between the first and second anterior filtration lines provided in parallel with each other. The system controls the switching part in accordance with dissolved oxygen content in the seawater taken in by the intake part, thereby improving the efficiency of seawater filtration with the ultrafiltration membranes.