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The pick-up, migration, deposition, and clogging behaviors of fine particles are ubiquitous in many engineering applications, including contaminant remediation. Deposition and clogging are detrimental to the efficiency of environmental remediation, and their mechanisms are yet to be elucidated. Two-dimensional microfluidic models were developed to simulate the pore structure of porous media with unified particle sizes in this study. Kaolin and bentonite suspensions were introduced to microfluidic chips to observe their particle deposition and clogging behaviors. Interactions between interparticle forces and particle velocity profiles were investigated via computational fluid dynamics and discrete element method simulations. The results showed that (1) only the velocity vector toward the micropillars and drag forces in the reverse direction were prone to deposition; (2) due to the negligible weight of particles, the Stokes number implied that inertia was not the controlling factor causing deposition; and (3) the salinity of the carrying fluid increased the bentonite deposition because of the shrinkage of the diffused electrical double layer and an increase in aggregation force, whereas it had little effect on kaolin deposition.