Provided is a fluid treatment system, including: a plurality of fluid channel devices arranged in series along a regular channel; a plurality of flow control valves each adjusting the flow rate of a treatment target fluid flowing into each of the plurality of fluid channel devices; a flow control valve provided on the upstream side of the plurality of fluid channel device and operable to change the flow rate of the treatment target fluid flowing into each of the plurality of fluid channel device; a bypass channel allowing the treatment target fluid to flow so as to bypass the fluid channel device in which abnormality has occurred, and a plurality of bypass selector valves selectable between a state of allowing the flow of the treatment target fluid in the bypass channel and a state of blocking the flow.