River dynamics are the key to fluvial systems not only in terms of how they work, but also with regard to the ecological, landscape, and environmental value of these systems. If a river is to be preserved as an ecosystem and an environmental corridor in the territory, it is mainly its hydro-geomorphological dynamics that have to be protected, because it is precisely them that will guarantee the protection of each and every element of the system and their relationships. This is the reason why the assessment of the hydro-geomorphological functioning of fluvial systems is essential to determine its environmental condition as well as its foreseeable trends. Thus, a hydro-geomorphological assessment index is proposed with the technical purpose of applying the Directive 2000/60/EU and the equally important scientific objective of improving the knowledge and diagnosis of fluvial systems, all this within the framework of the urgent and necessary search for solutions to its current environmental problems. The work presented includes methodological explanations for the application of the index, which is structured in three assessment parameters: 1) functional quality of the fluvial system, including a) naturalness of the discharge regime, b) sediment availability and mobility and, c) functionality of the floodplain; 2) channel quality, including a) naturalness of channel layout and morphology, b) continuity and naturalness of the riverbed and longitudinal and vertical processes and, c) naturalness of the riparian corridor and lateral mobility; and 3) quality of the riverbanks, including a) longitudinal continuity, b) width, structure, and naturalness and, c) cross-section interconnectivity.