A B S T R A C TWith increasing evidences of climate change affecting coastal waters, there is a strong need to understand future climate conditions and assess the potential responses of delicate coastal ecosystems. Results of climate change studies based on only one GCM-RCM combination should be interpreted with caution as results are highly dependent on the assumptions of the selected combination. In this study we examined the uncertainty in the hydrological and ecological parameters of the Zero river basin (ZRB) -Palude di Cona (PDC) coastal aquatic ecosystem generated by the adoption of an ensemble of climate projections from ten different combinations of General Circulation Model (GCM) -Regional Climate Model (RCM) under two emission scenarios (RCP4.5 and RCP8.5) implemented in the hydrological model (SWAT) and the ecological model (AQUATOX). The baseline period of 1983-2012 was used to identify climate change variations in two future periods: mid-century (2041-2070) and late-century (2071-2100) periods. SWAT outputs from the ensemble indicate a summer reduction in inorganic nitrogen loadings of 1-22% and a winter increase of 1-19%. Inorganic phosphorus loadings indicate a yearly increase of 32-61%. AQUATOX outputs from the ensemble show major changes in the summer period, with an increase in Chl-a concentration of 9-56%, a decrease in diatoms of 74-98% and an increase in cyanobacteria of 421-3590%. Obtained results confirm that the use of multiple GCM-RCM projections can provide a more robust assessment of climate change impacts on the hydrology and ecology of coastal waters, but at the same time highlight the large uncertainty of climate change-related impact studies, which can affect the decision-making processes regarding the management and preservation of sensitive aquatic ecosystems such as those in coastal areas.