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The clogging of a stream bed has a significant impact on the exchange of water between a river and groundwater, known as hyporheic exchange. Clogging issues in orifices influenced by fluid flow have long been a concern, particularly in understanding clogging mechanisms and particle dynamics. This study focuses on investigating the behavior of poly-dispersed particle systems in the Shanghai soft soil using a coupled lattice Boltzmann method and a discrete element method (LBM-DEM). A particle-orifice model was developed based on LBM-DEM to study the clogging problem. Three different orifice diameters with the same particle size distribution were set at a microscopic scale. The simulation results indicate that the primary form of clogging is the formation of particle domes, exhibiting distinct characteristics depending on orifice size. As the orifice size increases, clogging becomes more challenging. Interestingly, the flow rate of fluid passing through clogged orifices is quite complex, as it does not decrease significantly. The formation process of the particle structure shows significant randomness, posing challenges for quantitative analysis and experimental validation. This study provides insights into the initial stages of clogging formation, leading to a better understanding of hyporheic exchange phenomena in stream bed ecosystems. [ABSTRACT FROM AUTHOR]