Coastal vegetated habitats maintain highly diverse communities, where the contribution of macrophyte production is significant for macroinvertebrate primary consumers. In the brackish-waters of the Baltic Sea, the taxonomical diversity of different macrophytes includes both marine and limnic species. To study the basal food-web differences of two key vegetated habitat types, either dominated by a perennial brown macroalgae (Fucus vesiculosus) or by angiosperm plants, ¹³C and ¹⁵N compositions of different primary producers and macroinvertebrate consumers were examined, and their diets were estimated by Bayesian mixing models. Carbon isotope diversity of primary producers was high especially in the hard-bottom Fucus-dominated habitats, which was also reflected in a larger consumer isotope niche. However, consumer isotope niche among sites was similar within the same habitat type. Our models indicated that the perennial macrophyte dietary median contribution was about 25% for deposit feeders and omnivores in both habitat types, while epigrazers preferred filamentous algae (30–60%). The niche positions of the abundant clams L. balthica, M. arenaria and C. glaucum differed between the two habitats, but they showed only small (<10% units) differences in their macrophyte dietary contributions. The isotopic compositions of the dominating primary producer assemblage reflected significantly in the isotope niche structure of the associated primary consumers.