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Cation-intercalated graphene oxide (GO) membrane has emerged as a promising candidate for desalination applications as reverse osmosis (RO) membrane. This study constructs GO membranes with different cations (K+ or Mg2+) and investigates the potential of these membranes in boron removal via nonequilibrium molecular dynamics simulations. In the aquatic environment, boron can exist in the form of boric acid or borate ion, depending on the pH of the solution. As a result, this study considers two forms of boron. This study reveals that the GO membranes effectively reject negatively charged borate ions due to their bigger hydration shell and stronger electrostatic repulsion with the membrane than neutral boric acid molecules. Moreover, K+ ion intercalated GO membranes showed higher boron rejection than Mg2+ ion intercalated GO membranes owing to weaker electrostatic attraction of K+ ions with the boric acid (or borate ions). Additionally, a summary of the effects of oxygen-containing functional groups of the GO membrane on boron rejection is provided. Since the hydroxyl and epoxy functional groups interact with boric acid molecules more strongly, these molecules are prevented from permeating through the membrane. On the other hand, the permeation rate of borate ions declines because of their stronger interactions with the carboxyl functional groups. Furthermore, Mg2+ ion intercalated GO membranes exhibited higher water permeance, excellent Na+ rejection, and poor Cl− rejection compared to K+ ion intercalated GO membranes. • The effects of intercalated cations inside the GO layers on boron rejection are investigated. • GO membranes reject borate ions effectively when compared to boric acid. • The impact of oxygen-containing functional groups of GO membranes on boron rejection is presented. [ABSTRACT FROM AUTHOR]