The effects of climate warming and eutrophication on aquatic organisms are well established, but we lack a deep understanding of the selective mechanisms of fish communities towards eutrophication and warming in tandem. The aim of the study was to identify fish traits that were positively related to eutrophication and ongoing warming. The research was conducted for 19 years in the Dnipro River channel and floodplain water system of the “Dnipro-Orylskiy” Nature Reserve. Both categorical and continuous fish traits were considered. The study area is characterized by a more intense warming trend than the average for Europe, which reflects an increase in the maximum summer air temperature. At the same time, the concentration of chlorophyll-a had a monotonic tendency to decrease during the study period. Phytophilic, limnophilic, and freshwater fish species are increasing in abundance, while rheophilic and lithophilic fish are decreasing due to global warming. Fish species with greater vulnerability and resilience have selective advantages in terms of global warming. Pelagic fish species are the most resistant to eutrophication, while benthopelagic and phytolithophilic fish species are the most sensitive. Brackish-water demersal self-settled species of marine origin have a competitive advantage over other native freshwater species in the face of increasing symptoms of eutrophication and a warming climate.