This study assessed how changes in terms of temperature and precipitation might translate into changes in water availability and droughts in an area in a developing country with environmental interest. The hydrological model Soil and Water Assessment Tool (SWAT) was applied to analyze the impacts of climate change on water resources of the Guajoyo River Basin in El Salvador. El Salvador is in one of the most vulnerable regions in Latin America to the effects of climate change. The predicted future climate change by two climate change scenarios (RCP 4.5 and RCP 8.5) and five general circulation models (GCMs) were considered. A statistical analysis was performed to identify which GCM was better in terms of goodness of fit to variation in means and standard deviations of the historical series. A significant decreasing trend in precipitation and a significant increase in annual average temperatures were projected by the middle and the end of the twenty–first century. The results indicated a decreasing trend of the amount of water available and more severe droughts for future climate scenarios with respect to the base period (1975–2004). These findings will provide local water management authorities useful information in the face of climate change to help decision making.