This study aimed to assess the alterations in the community structure of macroinvertebrates associated with two seagrass-dwelling sponge species following a shift in the environmental conditions. Individuals of the sponge Amorphinopsis atlantica, whose optimal distribution is in areas exposed to wind-driven waves, were transplanted to a less exposed area and, contrarily, individuals of Haliclona implexiformis, whose optimal distribution is in less exposed areas, were transplanted to an exposed area. After 71 days, individuals of A. atlantica showed a decrease in the density (75.5%), family richness (29.8%), and diversity (22.2%) of associated macroinvertebrates regarding controls, whereas those of H. implexiformis showed an increase in the density (85.9%), family richness (57.7%), and diversity (20.8%). These changes were attributed to species turnover, recruitment of some associated taxa, and morphological changes in one of the host sponge species. In the exposed site, the associated communities were more influenced by the hydrodynamism and sedimentation rate, and in the protected site, by salinity and the concentrations of organic matter in surface sediments and the water column. Overall, this study highlights the complex interactions between environmental conditions and marine biodiversity, providing valuable data for the conservation and management of seagrass meadow ecosystems and their associated sponge communities.