This paper presents a mathematical model of the water level variation in the first pool of the Imperial de Aragón main irrigation canal - belonging to the Ebro Hydrographical Confederation - obtained by applying system identification tools. The complete system identification procedure, from experimental design to model validation, taking into account prior physical information, is developed. It is demonstrated that a linear second-order model with ARMAX structure and a time delay can adequately describe the dynamic behavior of an irrigation canal pool. The results of model validation show that the model obtained reproduces with high accuracy the observed data and that it can be applied for the design of effective control systems and/or for prediction purposes.