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Simple Summary In recent decades, the riverine ecosystems have been considered to evaluate the aquatic biological diversity, hydrological variations, and ecosystem services. However, climatic change scenarios and anthropogenic interventions are expected to shift from perennial to intermittent rivers with possible repercussion on aquatic biodiversity and human well-being. Our study identified a significant reduction in the Mediterranean intermittent river streamflow with an increase of zero flow days in the last decades. Furthermore, the aquatic invertebrates showed variations during the transition from drying to rewetting with a significantly changing species adapted to the flowing conditions (rheophilic taxa) to non-flowing water. The importance of the disconnected pools as refuges during the dry condition was recognised to protect some endemic species and contribute to the recolonisation after the rewetting events. Include these important aquatic ecosystems in management and conservancy policies is a challenge that will contribute to preserving the freshwater resources and the biological diversity for our future generations. Abstract Intermittent rivers and ephemeral streams (IRES) are increasingly studied because of their often-unique aquatic and terrestrial biodiversity, biogeochemical processes and associated ecosystem services. This study is the first to examine the hydrological, physicochemical and taxonomic variability during the dry-wet transition of an intermittent river in the Chilean Mediterranean Zone. Based on 30-years of river monitoring data and the TREHS tool, the hydrology of the river was characterised. Overall, the river shows a significant reduction in streamflow (−0.031 m3/s per year) and a substantial increase of zero flow days (+3.5 days per year). During the transition of hydrological states, variations were observed in the environmental conditions and invertebrate communities. During the drying phase, abundance, richness, and diversity were highest, while species turn-over was highest during base flow conditions. The disconnected pools and the flow resumption phases were characterised by high proportions of lentic taxa and non-insects, such as the endemic species of bivalves, gastropods, and crustaceans, highlighting the relevance of disconnected pools as refuges. Future climatic change scenarios are expected to impact further the hydrology of IRES, which could result in the loss of biodiversity. Biomonitoring and conservation programmes should acknowledge these important ecosystems.