Estuarine fish assemblages are undergoing rapid change due to invasions of non-native species and physicochemical alteration of their habitats. Here, we examine the novel fish assemblages of the upper San Francisco Estuary (SFE) by first placing the fishes into ecological assemblages (EAs) of species that co-occur based on salinity, macrohabitat, and diet. We then used the morphological characteristics of each species to place them into functional groups (FGs) or potentially functionally independent species (FIS). Our question was: are there native and non-native species that occupy a similar niche in ecomorphological space, and thus potentially interact? Then, based on our results, we sought to understand if there is evidence that native species are being displaced by non-native species. The 43 species examined were placed into 17 EAs of potentially interacting species. Within these EAs, we identified 13 FGs and 13 FIS based on ecomorphology. Six FGs contain both native and non-native species indicating organization independent of the origin of the species. However, in most cases the native species were present in low abundance or were in categories of risk. Five FGs contained just non-native species that were found mainly in altered habitats and two FGs contained just native species. Overall, both native and non-native species appear to form a novel assemblage, although the decline of some native species in the face of potential competitors and predators suggests the final assemblage has not yet been determined. In addition, ongoing alterations of the SFE ecosystem increase the likelihood that invasions of new species will continue, causing further changes to the assemblage.