This article addresses the identification of the nonlinear dynamics of the main pool of a laboratory hydraulic canal installed in the University of Castilla La Mancha. A new dynamic model has been developed by taking into account the measurement errors caused by the different parts of our experimental setup: (a) the nonlinearity associated to the input signal, which is caused by the movements of the upstream gate, is avoided by using a nonlinear equivalent upstream gate model, (b) the nonlinearity associated to the output signal, caused by the sensor’s resolution, is avoided by using a quantization model in the identification process, and (c) the nonlinear behaviour of the canal, which is related to the working flow regime, is taken into account considering two completely different models in function of the operating regime: the free and the submerged flows. The proposed technique of identification is based on the time-domain data. An input pseudo-random binary signal (PRBS) is designed depending on the parameters of an initially estimated linear model that was obtained by using a fundamental technique of identification. Fractional and integer order plus time delay models are used to approximate the responses of the main pool of the canal in its different flow regimes. An accurate model has been obtained, which is composed of two submodels: a first order plus time delay submodel that accurately describes the dynamics of the free flow and a fractional-order plus time delay submodel that properly describes the dynamics of the submerged flow.