A new method is proposed for controlling main irrigation canals with variable dynamical parameters based on robust fractional order controllers. A methodology for designing PID controllers robust to changes in the time delay and the gain is presented first. Then this method is generalized to design fractional controllers that exhibit the same robustness as the previous PID to time delay and gain changes, but are noticeably more robust to variations in the dominant time constant of the process. This method is applied to control main irrigation canals. Extensive numerical simulations using the dynamic model of a real canal were carried out. Then experimental results were obtained in a prototype canal that proved the effectiveness of the proposed control method in terms of performance and robustness.