This paper proposes a new methodology to design fractional integral controllers combined with Smith predictors, which are robust to high frequency model changes. In particular, special attention is paid to time delay changes. These controllers show also less sensitivity to high frequency measurement noise and disturbances than PI or PID controllers. This methodology is applied to design controllers for water distribution in a main irrigation canal pool. Simulated results of standard PI and PID controllers plus a Smith predictor, and the controller developed in this paper are compared when applied to the dynamical model of a real main irrigation canal pool showing that our controller exhibits better and more robust features than these. Moreover our controller is compared with other more complex control techniques as predictive control and robust H∞ controllers, exhibiting better or similar performances than these. © 2008 Elsevier Ltd. All rights reserved.