Abstract The emission and fate of methyl mercaptan from the residential complex treatment plant (RCTP) moving bed bioreactor (MBBR) process in the city of Al-Hur in Karbala governorate in Iraq were studied using the TOXCHEM 4.1 model. The release of odorous sulfur compounds from treatment plants harms workers and the surrounding area. Methyl mercaptan, in particular, is responsible for odors similar to rotten cabbage. The sensitivity analysis for the methyl compounds in the MBBR system was conducted based on the following factors: a large thick biofilm layer, the specific surface area of media, media fill fraction, and aeration flowrate. The model was validated via RMSE and R, which showed the model outputs are representatives of real-world observations. Degradation and emission were shown to be the two most important processes in the system. During the summer (32 °C) and winter (12 °C), about 13 and 10%, 2 and 4%, 0.5 and 1%, and 85 and 85% were emitted into the atmosphere, discharged with effluent, sorbed into sludge, and biodegraded, respectively. The overall concentrations of CH4S emitted in summer and winter were 1.78 and 1.38 ppm, respectively. Operating the MBBR system with a thick biofilm layer, a large specific surface area of media, a greater media fill fraction, and a low aeration rate contributed significantly to the decomposition of methyl mercaptan and thus decreased emission into the atmosphere. Finally, the TOXCHEM simulation accurately predicts the fate of CH4S and the emissions inherent to the MBBR system. The manipulation of the operating factors led to the improvement of the system and the reduction of methyl mercaptan gas emissions without the need to add units and chemical additives.