Most previous water quality studies oversimplified in-stream processes for modeling the fate and transport of critical organic contaminants, such as Polycyclic Aromatic Hydrocarbons (PAHs). Taking four selected PAHs as representative organic contaminants, we developed a numerical modeling framework using a Water Quality Analysis Simulation Program 8 (WASP8) and a well-established watershed model, i.e., Soil and Water Assessment Tool (SWAT) to: (1) address the influence of in-stream processes, including direct photolysis, volatilization, partitioning of PAHs to suspended solids, and DOC complexation processes on PAH concentrations; and (2) establish relationships between spatiotemporal distribution of environmental factors (e.g., ice coverage, water temperature, wind, and light attenuation), in-stream processes, and PAH concentrations at a watershed scale. Using calibrated SWAT and WASP8 models, we evaluated the impacts of seasonal changes in environmental factors on in-stream processes in the Muskeg River watershed, which is part of the Athabasca Oil Sands Region (AOSR), the third-largest crude oil reserves of the world in western Canada. Among four selected PAHs, simulation results suggest that Naphthalene primarily decay in the water through volatilization or direct photolysis. For Phenanthrene, Pyrene, and Chrysene, DOC complexation, volatilization, and direct photolysis all contribute to their decay in the water, with a strong dependence on seasonality. Model simulations indicated that direct photolysis and volatilization rates are meager in cold seasons, mainly due to low river temperature and ice coverage. However, these processes gradually resume when entering the warm season. In summary, the model simulation results suggest that critical in-stream processes such as direct photolysis, volatilization, and partitioning and their relationship with environmental factors should be considered when simulating the fate and transport of organic contaminants in the river systems. Our results also reveal that the relationship between environmental factors and fate processes affecting PAH concentrations can vary across a watershed and in different seasons.