There is a great deal of interest to determine the state and variations of water quality parameters in the lower Athabasca River (LAR) ecosystem, northern Alberta, Canada, due to industrial developments in the region. As a cold region river, the annual cycle of ice cover formation and breakup play a key role in water quality transformation and transportation processes. An integrated deterministic numerical modelling framework is developed and applied for long-term and detailed simulation of the state and variation (spatial and temporal) of major water quality constituents both in open-water and ice covered conditions in the lower Athabasca River (LAR). The framework is based on the a 1D and a 2D hydrodynamic and water quality models externally coupled with the 1D river ice process models to account for the cold season effects. The models are calibrated/validated using available measured data and applied for simulation of dissolved oxygen (DO) and nutrients (i.e., nitrogen and phosphorus). The results show the effect of winter ice cover on reducing the DO concentration, and a fluctuating temporal trend for DO and nutrients during summer periods with substantial differences in concentration between the main channel and flood plains. This numerical frame work can be the basis for future water quality scenario-based studies in the LAR.