Marine coastal areas are highly productive due to the presence of various inputs of organic matter, including terrestrial material, which fuels food webs. However, the ecological mechanisms underlying the productivity of benthic and demersal fish species in estuarine areas are poorly understood. By means of C and N stable isotope analysis and Bayesian mixing models, we investigated the trophic niches of three common fish species: Citharus linguatula, Pegusa lascaris (flatfish) and Liza ramada (mullet) in the Gulf of Gaeta (Italy). Fish were collected from the north-western area and the south-eastern area of the Gulf of Gaeta, the latter affected by organic inputs from the Garigliano River. The results highlighted the riverine terrestrial origin of the organic matter at the base of the food web in the south-eastern area and marine autochthonous input in the north-western area. All fish species increased their trophic specialisation in proximity to the river mouth. L. ramada specialised on seston of terrestrial origin, reducing its niche overlap with C. linguatula and P. lascaris. Away from the river mouth, all species were characterised by longer individuals, increased intraspecific diet variability and higher interspecific similarity in resource use. Organic input from the river represented a complementary trophic niche axis that enabled lower interspecific niche overlap in the south-eastern area, where fish populations were found at higher densities. In conclusion, this study provided information about the effects of the flow of material from the basal compartment up to abundant fish species in areas enriched by organic matter of varying origin.