A water treatment system having a biological treatment step (a secondary treatment step) and a membrane separation step (a tertiary treatment step), wherein a portion of the raw water to be treated and/or a portion of the primarily treated water in the pretreatment step are biologically treated and supplied into a reaction tank in the membrane separation step as the main channel system, while the remainder the raw water to be treated and/or the remainder of the primarily treated water in the pretreatment step are added together with a flocculating agent to the reaction tank in the membrane separation step, and then the membrane separation is conducted in the membrane separation step.