Understanding the effects of environmental stressors (e.g., potential changes in climate and land use) on ecological status is essential for freshwater management. The ecological response of rivers to stressors can be evaluated by several physico-chemical, biological, and hydromorphological elements as well as computer tools. In this study, an ecohydrological model based on SWAT (Soil and Water Assessment Tool) is used to investigate climate change impact on the ecological status of Albaida Valley Rivers. The predictions of five General Circulation Models (GCMs) each with four Representative Concentration Pathways (RCPs) are employed as input to the model for simulating several chemical and biological quality indicators (nitrate, ammonium, total phosphorus, and the IBMWP (Iberian Biological Monitoring Working Party) index) in three future periods (Near Future: 2025–2049, Mid Future: 2050–2074, and Far Future: 2075–2099). Based on chemical and biological status predicted with the model, the ecological status is determined at 14 representative sites. As a result of increased temperatures and decreased precipitations from most of GCMs projections, the model predicts decreased river discharge, increased concentrations of nutrients, and decreased values of IBMWP for future compared to the baseline period (2005–2017). While most representative sites have poor ecological status (10 sites with poor ecological status and four sites with bad ecological status) in the baseline, our model projects bad ecological status for most representative sites (four sites with poor ecological status and 10 sites with bad ecological status) under most emission scenarios in the future. It should be noted that the bad ecological status is projected for all 14 sites under the most extreme scenario (i.e., RCP8.5) in the Far Future. Despite the different emission scenarios, and all possible changes in water temperature and annual precipitation, our findings emphasize the urgent need for scientifically informed decisions to manage and preserve freshwaters.