The fate and transport processes of a toxic chemical such as atrazine, an herbicide, in a reservoir are significantly influenced by hydrodynamic regimes of the reservoir. The two-dimensional (2D) laterally-integrated hydrodynamics and mass transport model, CE-QUAL-W2, was enhanced by incorporating a submodel for toxic contaminants and applied to Saylorville Reservoir, Iowa. The submodel describes the physical, chemical, and biological processes and predicts unsteady vertical and longitudinal distributions of a toxic chemical. The simulation results from the enhanced 2D reservoir model were validated by measured temperatures and atrazine concentrations in the reservoir. Although a strong thermal stratification was not identified from both observed and predicted water temperatures, the spatial variation of atrazine concentrations was largely affected by seasonal flow circulation patterns in the reservoir. In particular, the results showed the effect of flow circulation on spatial distribution of atrazine during summer months as the river flow formed an underflow within the reservoir and resulted in greater concentrations near the surface of the reservoir. Atrazine concentrations in the reservoir peaked around the end of May and early June. A good agreement between predicted and observed times and magnitudes of peak concentrations was obtained. The use of time-variable decay rates of atrazine led to more accurate prediction of atrazine concentrations, while the use of a constant half-life (60 days) over the entire period resulted in a 40% overestimation of peak concentrations. The results provide a better understanding of the fate and transport of atrazine in the reservoir and information useful in the development of reservoir operation strategies with respect to timing, amount, and depth of withdrawal.