Pool scrubbing is conducted to remove contaminated aerosols/particles released from nuclear power generation systems in severe accidents. Gas-entrained particles pass through the pools in three stages: 1) injection into the pools through a vent, 2) decontamination process in bubbles rising in the pools, and 3) secondary entrainment into the atmosphere at the pool surface. The particle separations in the rising bubble swarm constitute the primary process for aerosol decontamination. The dynamics of the particles contained in the rising bubble swarm are crucial. Numerical modeling of particle transportation in bubbles in three-phase systems is complex and challenging. This study aimed to investigate the particle flow dynamics in scrubbing pools to understand the particle decontamination mechanism, which can guide equipment design to achieve high aerosol separation efficiency. In this study, particle decontamination in bubbles is simulated by using the Eulerian–Lagrangian method. This numerical method is used to investigate the mechanisms of flow dynamics, coagulation, and separation of particles in the bubbles, as well as the particle decontamination affected by the operation parameters such as the bubble velocity, and gas and particle properties. In addition, the decontamination factor is predicted for aerosol particles in the small bubbles of the rising swarm, which agrees with the calculated experimental DF of the bubble swarm.