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Supplying agricultural water has recently become more challenging due to increase in drought frequency in semi-arid regions. Unreliable supply water resources lead to inflow fluctuations in irrigation districts locating at the downstream part of the rivers. The conventional operation cannot handle the fluctuations effectively; therefore, water delivery to the off-takes is seriously compromised. In this study, the capability of decentralized Proportional-Integral (PI) and centralized Linear Quadratic Regulators (LQR) controllers were investigated to alleviate the effects of severe inflow fluctuations in the main irrigation canals operation. In this regard, the Roodasht North Branch (RNB) main canal, located in the central Iran, consisting of 24 reaches was selected as a test case. Mathematical operational model of the canal was coupled with the designed PI and LQR controllers. The performance of the controllers were evaluated under the normal and severe unpredictable inflow fluctuations scenarios. The results showed that the PI configuration was able to successfully deal with and handle the normal inflow fluctuations. Water delivery to the upstream and middle canal reaches was regulated reasonably well, while the downstream canal reaches were still slightly suffering from the inflow fluctuation. The LQR controller showed an outstanding performance in dealing with both normal and severe inflow fluctuation test scenarios. The controller optimally adjusted the gates accordingly to manage even the sever inflow fluctuation. The results of this study demonstrate capabilities of the control configurations in managing the inflow fluctuations in main canals which can help moving towards the urgent needs for improving the current canal operational performance.