Submersed aquatic vegetation (SAV) provides essential habitat and food to numerous coastal invertebrate species. In the eutrophic Baltic Sea, fast-growing drifting algae form extensive mats that can negatively impact SAV. However, these mats also offer additional habitat and food to epifauna. The aim of this study was to assess the effects of SAV and filamentous mats on epifaunal communities in shallow soft-bottom habitats around Gotland, Sweden, in the central Baltic Sea. We used generalised linear models (GLMs) to evaluate the influence of SAV vertical structure, biomass and macrophyte species richness (including macroalgae) and filamentous mat biomass on epifaunal community properties as well as on those of key grazer species. Diversity, vertical structure and biomass of SAV were positively associated with higher total epifaunal abundance and greater abundance gastropod grazers. In contrast, filamentous mats only increased gastropod abundance and biomass. In addition to introducing a rapid tool for quantifying vegetation structural complexity, this study highlights the selective effects of different habitat types on invertebrate communities in a relatively understudied region of the Baltic Sea. As warming temperatures and eutrophication promote filamentous mat growth, reducing nutrient pollution and protecting SAV will be crucial for sustaining abundant and diverse epifaunal communities.