High concentrations of 2-methylisoborneol (2-MIB) were reported during winter in the Paldang reservoir and North Han River, South Korea. The causes of the unusual taste and odor problems in the regulated river-reservoir system were not understood; however, a short-term solution is to flush out 2-MIB-rich water to secure water sources for over 20 million people. Approximately 150 million tons of water was released from upstream dams for 12 days (late November to early December 2018) to reduce the elevated levels of 2-MIB. Simultaneously, the spatio-temporal variations of the measured concentration of sample 2-MIB from five sites were simulated using a multi-dimensional hydrodynamics-based solute transport model to monitor the flushing effect. A modified environmental fluid dynamics code (EFDC) was adopted as the primary model framework. Five scenarios on the kinetic constants related to the characteristics of 2-MIB transport and behavior, such as conservative, net decay, and net production, were applied, and the results were compared. We found that the simulation errors on the elapsed times to satisfy the Korean drinking water monitoring standard (≤20 ngL−1) were smallest with the conservative dye transport option, indicating that the physical and biochemical characteristics of 2-MIB may not play an essential role.