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The estuary is an energetic area connecting the inland, river, and ocean. The migration of microplastics (MPs) in this highly complex area is tied to the entire ecosystem. In this study, the effects of cohesive SPM (clay) and noncohesive SPM (sand) on the vertical migration of positively buoyant MPs, polyethylene (PE), and negatively buoyant MPs, polytetrafluoroethylene (PTFE), in the estuarine environment under hydrodynamic disturbances were investigated. The settling of positively buoyant MPs was more reliant on the cohesive SPM compared to the settling of negatively buoyant MPs. Moreover, MPs interacting with the SPM mixture at a clay-to-sand ratio of 1:9 settled more efficiently than those interacting with clay alone. A significant positive correlation was observed between MP settling percentage and the salinity level. MP settling percentage was significantly negatively correlated with fluid shear stress for both types of MPs, meanwhile, negatively buoyant MPs were able to resist greater hydraulic disturbances. In the low-energy mixing state, for both types of MPs, the settling percentage reached about 50% in only 10 min. The resuspension process of MPs under hydrodynamic disturbances was also uncovered. Additionally, the migration and potential sites of MPs were described in the context of prevalent environmental phenomena in estuaries.