A ballast water intake and treatment system is disclosed, the system including a membrane treatment unit arranged in or on a ship hull for the separation of microorganisms of no smaller than a given size and organized to execute filtration during the intake of sea water or fresh water outside the hull into ballast tanks by the use of an intake pump installed consecutively with the membrane treatment unit. The system checks the invasion of microorganisms, etc. of no smaller than a given size during the intake of ballast water and allows ballast water free of microorganisms, etc. of no smaller than a given size to be fed into ballast tanks.