According to one embodiment, a seawater desalination system includes a membrane filtering pump, a first to third flowmeter, a filtering membrane, a high-pressure pump, a pressure gauge, a reverse osmosis membrane, a discharge valve and a control module. The membrane filtering pump outputs seawater according to a first control signal. The first flowmeter measures flow rate Q1. The high-pressure pump outputs filtered water from the filtering membrane according to a second control signal. The first pressure gauge measures pressure P1. The reverse osmosis membrane desalinates the filtered water into fresh water. The second flowmeter measures flow rate Q2. The third flowmeter measures flow rate Q3. The discharge valve discharges a high-concentration salt water according to a third control signal. The control module performs first, second, and third flow rate control with reference to the flow rate Q1, Q2 and Q3 and the pressure P1.