A CE-QUAL-W2 river hydrodynamics and water temperature model was developed for a 21-mile reach of the Illinois River including a 3-mile reach of the Fox River near the confluence with the Illinois River. Model outputs consist of streamflow, water velocity, water-surface elevation, and water temperature time series that can be used to simulate summer periods in years with and without extensive development of harmful algal blooms (HABs). These analyses may provide a better understanding of some complex factors that contribute to the development of HABs along the Illinois River. Such an understanding can ultimately provide the capability of more accurately predicting the timing and location of HABs along with determining potential mitigating activities to prevent or limit the size and duration of the algal blooms. Model scenarios documented in this data release include model calibration and validation, two water temperature scenarios with varying output intervals, and eight sensitivity analysis scenario runs.