The climate changes projected for the 21st century will have consequences on the hydrological response of catchments. These changes, and their consequences, are most uncertain in the transition zones. The study area, in the Bay of Biscay, is located in the transition zone of the European Atlantic region, where hydrological impact of climate change was scarcely studied. In order to address this scarcity, the hydrological impacts of climate change on river discharge were assessed. To do so, a hydrological modelling was carried out considering 16 climate scenarios that include 5 General Circulation Models (GCM) from the 5th report of the Coupled Model Intercomparison Project (CMIP5), 2 statistical downscaling methods and 2 Representative Concentration Pathways. Projections for future discharge (2011–2100) were divided into three 30-year horizons (2030s, 2060s and 2090s) and a comparison was made between these time horizons and the baseline (1961–2000). The results show that the downscaling method used resulted in a higher source of uncertainty than GCM itself. In addition, the uncertainties inherent to the methods used at all the levels do not affect the results equally along the year. In spite of those uncertainties, general trends for the 2090s predict seasonal discharge decreases by around −17% in autumn, −16% in spring, −11% in winter and −7% in summer. These results are in line with those predicted for the Atlantic region (France and the Iberian Peninsula). Trends for extreme flows were also analysed: the most significant show an increase in the duration (days) of low flows. From an environmental point of view, and considering the need to meet the objectives established by the Water Framework Directive (WFD), this will be a major challenge for the future planning on water management.