In this paper a fractional order model for an irrigation main canal is proposed. It is based on the experiments developed in a laboratory prototype of a hydraulic canal and the application of a direct system identification methodology. The hydraulic processes that take place in this canal are equivalent to those that occur in real main irrigation canals and the results obtained here can therefore be easily extended to real canals. The accuracy of the proposed fractional order model is compared by deriving two other integer-order models of the canal of a complexity similar to that proposed here. The parameters of these three mathematical models have been identified by minimizing the Integral Square Error (ISE) performance index existing between the models and the real-time experimental data obtained from the canal prototype. A comparison of the performances of these three models shows that the fractional-order model has the lowest error and therefore the higher accuracy. Experiments showed that our model outperformed the accuracy of the integer-order models by about 25%, which is a significant improvement as regards to capturing the canal dynamics.