Disclosed herein is a water controller system constructed such that water generated from a cathode of a direct methanol fuel cell system and carbon dioxide and an unreacted methanol solution generated from an anode of the direct methanol fuel cell system are introduced into the water controller system, the carbon dioxide is discharged out of the water controller system, and the methanol solution is circulated to the corresponding electrode so as to reuse the methanol solution. The water controller system includes a specific-structure floating member having a gas exhaust port, a gas/solution inlet port, and an outlet port. The water controller system further includes a flexible inlet pipe, a flexible outlet pipe, and a flexible exhaust pipe, which are connected to the floating member. The water controller system for fuel cells has the effects of reusing an unreacted methanol solution discharged from the fuel cell, being normally operated even when the water controller system is inclined, and uniformly maintaining the amount of water and methanol in the water controller system.