Climate change represents a major challenge for the management of native fish communities in Mediterranean rivers, as reductions in discharge may lead to a decrease in passability through small barriers such as weirs, both in temporary and perennial rivers. Through hydraulic modelling, we investigated how discharges from a large hydropower plant in the Tagus River are expected to affect the passability of native freshwater fish species through a rock weir (Pego, Portugal), equipped with a nature-like fish ramp. We considered not only mean daily discharge values retrieved from nearby gauging stations (1991–2005) for our flow datasets, but also predicted discharge values based on climatic projections (RCP) until the end of the century (2071–2100) for the Tagus River. Results showed that a minimum flow of 3 m3 s−1 may be required to ensure the passability of all species through the ramp and that passability was significantly lower in the RCP scenarios than in the historical scenario. This study suggests that climate change may reduce the passability of native fish species in weirs, meaning that the construction of small barriers in rivers should consider the decreases in discharge predicted from global change scenarios for the suitable management of fish populations.