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CE-QUAL-W2 is widely used for simulating hydrodynamics and water quality of the aquatic environments. Currently, the model calibration is mainly based on trial and error, and therefore it is subject to the knowledge and experience of users. The Particle Swarm Optimization (PSO) algorithm has been tested for automatic calibration of CE-QUAL-W2, but it has an issue of prematurely converging to a local optimum. In this study, we proposed an Improved Global-Best Harmony Search (IGHS) algorithm to automatically calibrate the CE-QUAL-W2 model to overcome these shortcomings. We tested the performance of the IGHS calibration method by simulating water temperature of Devils Lake, North Dakota, which agreed with field observations with R2 = 0.98, and RMSE = 1.23 and 0.77 °C for calibration (2008–2011) and validation (2011–2016) periods, respectively. The same comparison, but with the PSO-calibrated CE-QUAL-W2 model, produced R2 = 0.98 and Root Mean Squared Error (RMSE) = 1.33 and 0.91 °C. Between the two calibration methods, the CE-QUAL-W2 model calibrated by the IGHS method could lower the RMSE in water temperature simulation by approximately 7–15%.