Numerical modelling is becoming a major tool for supporting environmental studies at different scales, thanks to the capability of up-to-date codes in reproducing the natural behaviour in a quite reliable manner. In evaluating the habitat diversity of anthropized rivers, however, many issues are rising because of the intrinsic complexity of the processes involved. Using a reach of the Po River in Italy as a case study, the present works aims to provide an estimate of the changes of the Eco-Environmental Diversity as a response to different constant flow discharges. The goals are achieved by means of two solvers of the iRIC suite, applied in sequence to firstly simulate the fluvial hydrodynamics and subsequently provide an estimate of the habitat conditions. Despite the simplifications intrinsically present in the models and the ones introduced for practical purposes, the results pointed out that the reduction of the flow discharge recently observed can threat the overall biological status of the river. Because of the modelling uncertainties, on the other side, these preliminary outcomes show the need for more research, both in terms of data acquisition and numerical schematization, for adequately evaluate the effects of transient hydrology on the river ecosystems. Moreover, additional field surveys are necessary to calibrate and validate the used model for having sufficiently reliable estimates.