Feed spacer biofouling is a major challenge in membrane processes such as nanofiltration and reverse osmosis. The bubbling of gas using air can be effective in partially controlling biofouling, but additional chemical control is still needed, and pressurized air systems can be difficult to integrate into existing systems. A simpler approach that combines both bubbling and cleaning was developed here on the basis of intermittently adding a low concentration hydrogen peroxide (H2O2) to the feedwater. With periodic dosing (every 12 h) of 0.3% (w/w) H2O2, no detectable biofouling occurred after 10 days of operation, while biofouling was evident without H2O2 dosing. A single dose of 0.3% (w/w) H2O2 to prefouled spacers and membranes rapidly reduced biofouling, with decreased feed channel differential pressures of 69% (CuO spacer) and 54% (polypropylene spacer). The control of biofouling mainly resulted from bubble production when H2O2 dissociated to shear biofilms off the spacers. Using a CuO spacer did not impact biofouling, suggesting that additional cleaning based on hydroxyl radical formation via Fenton-reaction was not necessary. The use of H2O2 alone had the combined advantages of physically shearing off biofilms from spacers and chemically killing bacteria, while providing a low cost approach for biofouling control in membrane-based desalination processes.