Graphene oxide (GO)-based membranes formed by stacked nano-scale GO layers can be used to separate contaminants from the water via filtration. The membrane surface and permeation performance are altered by different filtration solutions. This study presented a facile vacuum-assisted approach of preparing a GO-Fe membrane by bonding between multivalent Fe and oxygenated functional groups on the membrane surface. Different solutions including water (pH 7.0), hydrogen peroxide (H2O2, pH 4.5), sulfuric acid (H2SO4, pH 3.0), and sodium hydroxide (NaOH, pH 9.7) were used. The impact of filtration on the membrane surface characteristics and permeation flux was investigated. In the results, filtration using water and H2SO4 exhibited the highest and lowest fluxes, respectively. Water filtration increased the O-H component of the membrane by hydration and improved the permeation flux (109.5 L m−2h−1 bar−1). However, this also potentially increased the interlayer distance of the membrane and reduced its molecule rejection rates. H2SO4 filtration destructed the membrane surface by enhancing the release of Fe. Filtration with H2O2 and NaOH maintained moderated spacing and permeation fluxes of the membrane by increasing the rates of oxygenation and protonation, respectively. The findings provide insights into how different types of solutions affect the stability and surface characteristics of a GO-based membrane modified by a multivalent cation.