To provide a membrane separation device for separating bacteria in seawater which controls the increase of the pressure difference of a membrane produced between the inlet and outlet of a membrane module for removing bacteria in seawater to obtain filtrate for washing fish and shellfish, prevents the re-development of the bacteria in a filtrate storage tank, can elongate a membrane backwashing time, and reduces the bacteria in the storage tank.

The first water level sensor is arranged on the upper side of the filtrate storage tank, the second water level sensor is arranged on the lower side of the tank, and piping which starts from the bottom of the tank and returns to a raw water tank through a membrane treatment water supply pump is installed. When the level of the filtrate is brought up to the position of the first water level sensor, the filtrate is returned to the raw water tank and filtered again. When the water level of the filtrate storage tank is brought down to the position of the second water level sensor, ordinary filtration is done.