As the effects of climate change continue to intensify, non-native species are becoming more prevalent in estuarine ecosystems. This has implications for the taxonomic and functional diversity of fish communities. Historically, biodiversity has been a synonym of taxonomic diversity, however this approach often fails to provide accurate insights on ecosystem functioning and resilience. To better understand how climate change is impacting fishes and their traits’ composition, a long-term dataset from Minho Estuary (NW Iberian Peninsula) fish assemblage was analyzed. The results suggest that climate change and extreme weather events altered the prevailing trait modalities of fishes, which led to the overall decrease in functional diversity of the fish assemblage over the course of a decade. This decrease is associated to the loss of some trait modalities that are exclusively found in native species. On the other hand, the invasive species added novel traits associated with the conditions of high temperatures and low precipitation regime currently observed in the studied area. Our results highlight that the shift in the presence and dominance of some traits is directly influenced by climatic changes. Also, despite the addition of novel modalities by the invasive species, the fish assemblage is now less functional and taxonomically diverse than previously.