This paper presents the design of a robust fractional order controller-which we denote as FPI controller since it can be regarded as a generalization of the standard PI controller-for effective control of water distribution in irrigation main canal pools characterized by timevarying dynamical parameters. Interest in such robust fractional order controller is justified by the fact that dynamical parameters of irrigation main canal pools may change drastically according to their operating discharge regimes. The FPI controller designed was installed in a PLC SIMATIC S-7 300, and was real-time implemented in the first pool of the Imperial de Aragon main canal, belonging to the Ebro Hydrographical Confederation (Spain). Realtime experiments were carried out with equivalent-in the sense of exhibiting the same closed loop dynamics for the nominal plant specifications-FPI and PI controllers. They showed a better performance and robustness of the FPI controller when large canal parameters variations were produced, that which facilitates to achieve a bigger speed of response, to satisfy in an operative way the demands of the users, as well as to minimize the losses for concept of operation of the available hydraulic resources.