In this paper a two-input, two-output (TITO) fractional order mathematical model of a laboratory prototype of a hydraulic canal is proposed. This canal is made up of two pools that have a strong interaction between them. The inputs of the TITO model are the pump flow and the opening of an intermediate gate, and the two outputs are the water levels in the two pools. Based on the experiments developed in a laboratory prototype the parameters of the mathematical models have been identified. Then, considering the TITO model, a first control loop of the pump is closed to reproduce real-world conditions in which the water level of the first pool is not dependent on the opening of the upstream gate, thus leading to an equivalent single input, single output (SISO) system. The comparison of the resulting system with the classical first order systems typically utilized to model hydraulic canals shows that the proposed model has significantly lower error: about 50%, and, therefore, higher accuracy in capturing the canal dynamics. This model has also been utilized to optimize the design of the controller of the pump of the canal, thus achieving a faster response to step commands and thus minimizing the interaction between the two pools of the experimental platform.