The paucity of data on non-indigenous marine species is a particular challenge for understanding the ecology of invasions and prioritising conservation and research efforts in marine ecosystems. Marenzelleria spp. are amongst the most successful non-native benthic species in the Baltic Sea during recent decades. We used stable isotope analysis (SIA) to test the hypothesis that the dominance of polychaete worm Marenzelleria arctia in the zoobenthos of the Neva Estuary after its invasion in the late 2000s is related to the position of this species in the benthic food webs. The trend towards a gradual decrease in the biomass of Marenzelleria worms was observed during 2014–2020, probably due to significant negative relationships between the biomass of oligochaetes and polychaetes, both of which, according to SIA, primarily use allochthonous organic carbon for their production. The biomass of benthic crustaceans practically did not change and remained very low. The SIA showed that, in contrast to the native crustacean Monoporeia affinis, polychates are practically not consumed either by the main invertebrate predator Saduria entomon, which preys on M. affinis, oligochaetes and larvae of chironomids or by benthivorous fish that prefer native benthic crustaceans. A hypothetical model for the position and functional role of M. arctia in the bottom food web is presented and discussed. According the model, the invasion of M. arctia has created an offshoot food chain in the Estuary food webs. The former dominant food webs, associated with native crustaceans, are now poorly developed. The lack of top-down control obviously contributes to the significant development of the Marenzelleria food chain, which, unlike native food chains, does not provide energy transfer from autochthonous and allochthonous organic matter to the upper trophic levels. The study showed that an alien species, without displacing native species, can significantly change the structure of food webs, creating blind offshoots of the food chain.