Microplastics are ubiquitous pollutants in oceans, rivers, lakes, estuaries, and coastal areas, and pose a serious threat to aquatic ecology and natural ecosystems. Predicting the fate and transport of microplastics in these water systems, which are typically driven by complex hydrodynamic patterns, is essential for understanding accumulation zones, pathways, and potential sources and necessary for decision-making, remediation, and recovery activities. Numerical models based on the Eulerian–Lagrangian approach have effectively demonstrated robustness in predicting the evolution of microplastics in aquatic environments. An innovative three-dimensional (3D) ray tracing (RT) model over unstructured grids to simulate the movement of particulate matter in water is utilized in this study (Ghazizadeh et al. in Comput Phys Commun 307:109423 (2025), [1]). This model (CaMPSim-3D) has been integrated into the 3D numerical particle tracking model (PTM) previously developed at the National Research Council of Canada for predicting the fate and transport of microplastics in rivers and coastal areas. The PTM has shown superiority in terms of computational efficiency compared to the existing models and is not reliant on mesh size. Additionally, the upgraded model is able to account for vertical changes in particle coordinates caused by tides. Furthermore, the PTM is capable of considering particle interactions with the shoreline and seabed during the tidal cycle by applying wet-dry conditions, particle sedimentation, and the beaching and washout processes. In this study, the PTM is applied in a real-world case study to predict the transport and accumulation zones of microplastics in the Saguenay Fjord. Up to 20 million particles are released in the Fjord. Particle concentration in 2 zones is studied and the normalized concentration over the entire computational domain is demonstrated.