This paper studies the migration and deposition of suspended particles in porous media. This problem results from the fact that during the operation of a groundwater source heat pump, the recharging process will contribute to the impairment of soil permeability. A coupling lattice Boltzmann method, discrete element method and immersed moving boundary method were used to investigate the migration of particles in porous media. The DKT (Drifting, Kissing, Tumbling) phenomena were employed to validate our program. The coupled effects of concentration, flow rate and pH on the clogging mechanism of the porous media were analyzed. Results show that, due to the repulsive barrier between the particles and porous media, there is a critical velocity. At a low flow rate, the deposition ratio increases with the increase in velocity. Beyond the critical velocity, the deposition ratio decreases when the velocity increases due to higher shear force. Permeability impairment increases with the increase in concentration, especially in the low flow rate condition. Changes in pH mainly affect the repulsive barrier. For a low flow rate, the decrease in repulsive barrier greatly promotes the deposition of particles. Under the condition of favorable deposition, the increase in flow rate reduces the deposition phenomenon. Under the condition of unfavorable deposition, the lower flow rate condition has a lower deposition ratio. The process of particle deposition and the dynamic motion after deposition were observed such as particles gliding over the surface. Accumulated particles in the downstream form bridges and hinder fluid flow. At a high flow rate, strong shear force is more capable of destroying bridges and recovering permeability. Adsorbed particles glide on the surface of the grain and deposit in the downstream. This paper aims to help understanding of the micro-events of particle deposition and the clogging process.