This paper proposes a new strategy for the control of water distribution in an irrigation main canal pool characterized by large time-varying time delays. Time delays may change drastically in an irrigation main canal pool as a consequence of variations in its hydraulic operation regime. An original methodology is developed to design fractional order PI controllers combined with Smith predictors that yield control systems which are robust to changes in the process time delay. This methodology is applied to solve the problem of effective water distribution control in an irrigation main canal pool. Simulated results of standard PI and PID controllers plus a Smith predictor are compared with the controller developed in this paper when applied to the dynamic model of a real irrigation main canal pool. The simulation results show that the proposed controller outperforms standard controllers in terms of performance and robustness.