Warming of the planet is indisputable and will lead to more frequent extreme events, such as droughts. From June 2003 to March 2008, the effects of variations in river flow, associated with drought conditions, were studied in the fish assemblage of the Mondego estuary, Portugal. Over this time, two distinct hydrological periods were identified: non-drought years and drought years, with consistent changes in the fish assemblages. In the drought years, salinity increased inside the estuary, displacing the estuarine brackish habitats to more upstream areas. During this period, new marine adventitious species were found mainly in the most downstream areas, while the freshwater species disappeared from the Mondego estuary catchment area. For the marine estuarine-dependent species that use estuaries as nursery areas, a decrease in abundance was observed during the drought years, owing to the decrease in freshwater flow and reduced river plume to the coastal area. In non-drought years, there were higher densities of most species and the more important species of the fish community. Our work shows that extreme events such as droughts, related to climatic changes, influenced the structure and composition of the Mondego estuary fish assemblages, and should be further considered when undertaking management plans for transitional waters.