Most rivers around the Mediterranean region, regardless of size, are interrupted by human induced barriers. Although various studies have been conducted to investigate the impacts of reservoirs on undisrupted freshwater biota, what kind of effects they exert on the distribution of freshwater fish assemblages with respect to the presence of invasive species remains to be answered. To attend to this research need, the Karamenderes River, which is disrupted by the Bayramic Reservoir, was selected as the research site. Relying on the river continuum concept (RCC), we hypothesized that fish assemblages in a given river would demonstrate a gradual downstream change unless the river is interrupted by any reservoir. The ad hoc unweighted pair group method with arithmetic means (UPGMA) agglomerative hierarchical cluster analyses revealed 11 fish assemblages 100 km down the studied river, which is characterized by four environmental gradients. Besides, co-occurrence network analyses were performed to gain a better understanding of the constructs of the observed fish assemblages. The analyses yielded two distinct clusters along the river and showed that the Bayramic Reservoir had no decisive part in the spatial clustering of these fish assemblages. The migratory species Anguilla anguilla was found only in and around the river mouth area. The co-occurrence network analyses indicated that the freshwater, estuarine and introduced species were observable in distinct groups. It is notable that the non-native Cyprinus carpio and invasive Carassius gibelio were determined in the native freshwater fish species module. The research evidenced that the reservoir had a triple effect, that is, a migration barrier to migratory fish species, a donor facilitating invasion, and a cause of homogenization of river fish assemblages along the river. The results suggest that the impact of the reservoir should be assessed in view of multiple nested model and fish passageways and controlling invasive species are two contradictory problems as far as the impacts of reservoirs are concerned. Therefore, river management should be performed in a way to allow the native migratory species to migrate freely while preventing the introduced species from moving upstream or downstream to preserve and promote rivers' heterogeneity.