This paper proposes a new technique for designing fractional order controllers applied to the automation of main canal pools of a water irrigation systems. As large variation of all the plant parameters is present in such systems, a fractional order PIα controller combined with a Smith Predictor is designed using time domain specifications. The designed controller is compared with the standard Smith Predictor combined with PI. All these controllers are tuned to fulfil the same time specifications in the case of canal nominal dynamics. In some canals the plant parameters may experience large changes that diminish the performance, and even can unstabilize the closed-loop system. Then the PIα controller is designed to maximize the robustness to variations in these parameters. Simulated results show the robustness improvements achieved with this controller compared with a conventional PI controller1. © 2011 IFAC.