A combined experimental and molecular dynamics study revealed the role of oxygen debris (ODs) and functional groups on the nanofiltration performance of a graphene oxide (GO) membrane. A NaOH treatment removed ODs adsorbed onto the graphene oxide (DGO). COOH-decorated GO (CGO) was prepared by controlling the oxidation time of Hummer's method, resulting in 45% of carbons with a COOH group. The water permeance of the prepared GO membrane without ODs was 1 order of magnitude greater than that of GO membranes in our experiments: 1.24, 1.59, and 14.7 L m(-2) h(-1) bar(-1) for GO, CGO, and DGO. However, the rejection of dye molecules below 1 nm in size was dramatically reduced without ODs, indicating that ODs play a critical role in rejecting molecules below 1 nm in size because of electrostatic and hydrogen bonding interactions and by narrowing the effective interlayer spacing, as noted in molecular simulations. Additionally, the CGO membrane displayed a similar separation performance compared to common GO membrane mainly decorated with OH and epoxy.