The FHARMOR project aims to explore new modeling and river survey techniques to improve current habitat simulation and evaluation methodologies. The research objectives are in line with the European Commission “Guidance document on Ecological Flows (Eflows)” for the implementation of the Water Framework Directive, which stresses on using information of river habitats (in terms of quality, quantity and distribution) as a metric to quantify the impact of hydromorphological alterations. Furthermore, as normatively defined by Annex V 1.2 of the WFD, biological assessment methods alone are not sufficient to guarantee that hydro-morphological pressures have no significant impact of water body status. This potential flaw of biological indicators is particularly important to be considered in Alpine rivers, where biological quality elements may indicate a good status whereas data from hydrological monitoring indicate that the water body is subject to a significant alteration of the flow regime.