Numerical modelling is becoming a major tool for supporting environmental studies at different scales, thanks to the ability of up-to-date codes to reproduce the complex mechanisms of the natural environment in quite a reliable manner. In evaluating the habitat diversity of anthropized rivers, however, many issues are rising because of the intrinsic complexity of the physical processes involved and the limitations associated with numerical models. Using a reach of the Po River in Italy as a case study, the present works aims to provide a qualitative description of the changes of the Eco-Environmental Diversity index as a response to different constant flow discharges typically observed along this reach. The goals are achieved by means of two solvers of the freeware iRIC suite, applied in cascade to first simulate the 2D fluvial hydrodynamics and subsequently provide a qualitative estimate of the habitat conditions. Despite the several simplifications intrinsically present in the modelling cascade and the ones introduced for practical purposes, the results show that an extremely strong and long-lasting reduction of the flow discharge, like the one very recently observed, can ultimately threaten the overall biological status of the river. Because of the modelling uncertainties, these preliminary outcomes are only qualitative and show the need for more research, both in terms of data acquisition and numerical schematization, to adequately and quantitatively evaluate the effects of transient hydrology on the river ecosystems. Moreover, additional field surveys are necessary to calibrate and validate the used biological parameters, aiming to obtain sufficiently reliable estimates.