Water temperature is an important indicator for biodiversity and ecosystem sustainability. In this study, a simplified equilibrium temperature model was incorporated into the CE-QUAL-W2 (W2) model. This model is easy to implement, needing fewer meteorological variables and no parameter calibration. The model performance was evaluated using observed data from four stations on the Lower Minnesota River. Results show that the simplified equilibrium temperature model performed as well as the original equilibrium temperature model and the term-by-term process model for water temperature predictions with the values of the coefficient of determination (R2), Nash–Sutcliffe Efficiency (NSE), and Percent Error (PE) in the accepted range (R2 = 0.974, NSE = 0.972, PE = 1.377%). The impact of the water temperature on Carbonaceous Biochemical Oxygen Demand (CBOD) concentrations under three different water temperature models was evaluated, and results show that the monthly averaged CBOD concentrations of the simplified equilibrium temperature model were almost the same as that of the term-by-term approach. For all the four calibration stations, the simplified equilibrium temperature approach performs better than the other two models for dissolved oxygen simulation (R2 = 0.791, NSE = 0.65, PE = 7.596%), which indicates that the simplified equilibrium temperature model can be a potential tool to simulate water temperature for water quality modelling.