We examined the relative importance of landscape features on estuarine fish trophic structure and dependence on terrestrial organic matter (OM_terr) in four barrier island lagoon systems along the Alaskan Beaufort Sea coast. Our study compared two relatively large lagoon systems characterized by high river discharge and relatively free ocean water exchanges (central region near Prudhoe Bay, Alaska) with two highly protected lagoons characterized by low river discharge and limited exchange with ocean waters (eastern region near Kaktovik, Alaska). We hypothesized that freshwater discharge would be a strong determinant of food web structure for both resident marine and diadromous fishes if more discharge increases availability of OM_terr relative to lagoons with limited or no river inputs. To consider differences in trophic characteristics in fishes between study regions, we estimated community-wide measures of trophic structure (hereafter, community metrics) and the relative use of OM_terr from mixing models using stable isotope composition (δ¹³C and δ¹⁵N; muscle tissue) among 12 species and identified the influences of region and body size. Fish captured in lagoons well protected by barrier islands had more distinct and diverse isotopic niches relative to those in more exposed lagoons based on community metrics. The use of OM_terr by nearshore fishes in both regions was substantial and was >50% for diadromous species. Between regions, OM_terr use differed in 6 of the 8 species considered but was not consistently higher in one region. The relative importance of OM_terr varied with fish size in 7 of 10 species considered, with more OM_terr used by smaller individuals. This work highlights the importance of OM_terr to Arctic fishes and fisheries, some of which are of subsistence importance, even when feeding grounds are primarily marine. We propose that landscape features, particularly barrier islands, play an important role in structuring nearshore food webs. Barrier islands may provide a previously undocumented ecosystem service of increasing food web complexity, which may promote system resilience.