Alien species and bottom trawl fisheries are of significant concern in the Eastern Mediterranean as both can put pressure on coastal systems whilst some alien species also constitute an important component of the trawl catches. Using an Ecopath model representing the Gulf of Mersin (Northeastern Mediterranean) for the period September 2009 to September 2013, this study describes the impacts of alien species and bottom trawl fisheries on the structure and functioning of this Northeastern Mediterranean food web. Our results show that the increase in alien species has had an important ecological impact on ecosystem structure and function. The alien species have had mostly negative impacts on native taxa, and trawl fisheries may have helped some alien species gain an advantage over native species, particularly at lower trophic levels. The Mixed Trophic Impact analysis showed that trawling and trawl discards had a noticeable direct and indirect impact on the food web, to the extent that trawling now affects the ecological role of the alien species. The cumulative overall impact of alien demersal functional groups on the pelagic domain, and vice versa suggest that alien species now play a role in benthic-pelagic coupling, and that this role is mediated by the fisheries. These results support the idea that alien species and trawling are now both important factors in structuring the Northeastern Mediterranean food web. It will thus be critical to consider both factors, as well as their interactions, when developing ecosystem-based management approaches for the region.