Hydraulically irreversible membrane fouling is a major problem encountered during membrane-based water purification. Membrane foulants present large hydrophobic fractions, with humic acid (HA) being a prevalent example of hydrophobic natural organic matter. Furthermore, HA contains numerous aromatic rings (π electrons), and its hydrophobic interactions are a major cause of irreversible membrane fouling. To address this issue, in this study, we used the cation-π interaction, which is a strong noncovalent, competitive interaction present in water. Because the strength of cation-π interactions depends on the combination of cations and π molecules, utilizing the appropriate cations will effectively remove irreversible fouling caused by hydrophobic HA. We performed macroscale experiments to determine the cleaning potential of the test cations, nanomechanically analyzed the changes in HA cohesion caused by the test cations using a surface force apparatus and an atomic force microscope, and used molecular dynamics simulations to elucidate the HA removal mechanism of test studied cations. We found that the addition of 1-ethyl-3-methylimidazolium, an imidazolium cation with an aromatic moiety, effectively removed the HA layer by weakening its cohesion, and the size, hydrophobicity, and polarity of the HA layer synergistically affected the HA removal mechanism based on the cation-π interactions.