Species-specific isolation of microsized entities such as microplastics and resistant bacteria from waste streams is becoming a growing environmental challenge. By studying the on-flow immobilization of micron-sized polystyrene particles onto functionalized silica surfaces, we ascertain if supramolecular host-guest chemistry in aqueous solutions can provide an alternative technology for water purification. Polystyrene particles were modified with different degrees of adamantane (guest) molecules, and silica surfaces were patterned with β-cyclodextrin (β-CD, host) through microcontact printing (μCP). The latter was exposed to solutions of these particles flowing at different speeds, allowing us to study the effect of flow rate and multivalency on particle binding to the surface. The obtained binding profile was correlated with Comsol simulations. We also observed that particle binding is directly aligned with particle's ability to form host-guest interactions with the β-CD-patterned surface, as particle binding to the functionalized glass surface increased with higher adamantane load on the polystyrene particle surface. Because of the noncovalent character of these interactions, immobilization is reversible and modified β-CD surfaces can be recycled, which provides a positive outlook for their incorporation in water purification systems.