The fiumara environment, as typical intermittent/ephemeral stream within the semi-arid Mediterranean environment area, is characterised by a persistent “non-equilibrium” status, due to the high spatial and temporal variability of the hydro-geomorphological, climatic and edaphic features. Consequently, the schematisation of a reference condition to guide the assessment of the ecological quality of fiumara context is a very complex issue. The available index-based methodologies can eventually lead to recognise negative ecological status even in presence of high levels of naturalness. In this regard, in order to help the recognition of more adherent reference condition for these peculiar hydro-systems, a multi-disciplinary analysis of both natural forcing feature and their interaction with the fluvial ecosystem has been carried out, and a set of representative case studies with and without human pressure were selected. Here, evaluation indexes, commonly used in the literature, were applied and their limitation in capturing the peculiar eco-hydrological and geomorphological dynamics was identified. Finally, a suitably defined sub-index was proposed and integrated into a pre-existing index for a better assessment of fiumare environments.