Storing water in main irrigation canal reaches could be an influential strategy to improve the existing operational activities in the irrigation canals. However, the control of such a canal system will become much more complicated due to freeboards of the reaches temporarily decreasing. In this paper, Model Predictive Control (MPC) is applied to control the water level of an accurate model of a realistic main canal, which consists of 13 canal reaches, using an in-line storage operational strategy. Four different test scenarios are selected to cover a range of conventional to unconventional operational strategies by imposing limitations on the head-gate opening. Different target bands are created between the predefined allowed maximum and minimum water level for the canal reaches and the MPC is obliged to keep the water levels within these ranges. The results show that the in-line storage improves current operational performance of the canal system by compensating the existing delay times of flow t...