Anthropogenic impacts cause habitat losses and reduce biodiversity in marine coastal habitats. Coastal macroalgae beds and their associate invertebrates are highly susceptible to environmental contamination. This study evaluated the differences in diversity parameters of Sargassum-associated gastropod and amphipod assemblages in areas located at different distances from a pollution source in a semi-enclosed, highly impacted bay, with the concentration of heavy metals in benthic Sargassum spp. as a contamination parameter. The Sargassum collected from sites closer to the source of contamination had higher concentrations of Cu, Zn and Fe. Rarefaction curves demonstrated that gastropod assemblages had significantly lower species richness and diversity at sites closest to the pollution source and regression analysis showed that lower diversity indexes and lower abundance of the main species were correlated with higher levels of most heavy metal concentrations in Sargassum. Amphipod did not present a clear pattern of diversity differentiation, and no correlation of the most abundant species with metal concentrations, even though these animals are known to be sensitive to metal contamination. This study highlights the importance of simultaneously studying different taxonomic groups in order to better understand anthropogenic impacts in marine environments and shows that macroalgae-associated gastropod assemblages are a potential indicator of marine pollution in semi-enclosed areas.