In this study, the water quality of the Bahmanshir River and its water channels where Choebdeh Shrimp Farms (the largest shrimp culture complex in Iran) are located were simulated using MIKE11 software. First, an integrated hydraulic and salinity model of the river and its water channels was developed. Then, Manning and dispersion coefficients of the river were calibrated and validated. The most important parameters in the water quality model were determined by sensitivity analysis and these parameters were calibrated using in situ measured water quality data. The errors of salinity, temperature, nitrate, ammonia and dissolved oxygen (DO) models in the verification step were 7.9, 1.2, 0.34, 0.79 and 12%, respectively. Then, two scenarios were applied to the river and the effects of these scenarios on the water quality of the river and its channels were evaluated. The results demonstrated that the site selection of the shrimp culture complex had been performed well because different scenarios could not affect the water quality in the channels. Finally, the water quality in the channels was compared with the standard values of shrimp survival parameters. All of the parameters in the channels were in the range of standard values except DO, which was slightly under the standard value.