Seagrasses enhance coastal regions by providing valuable environmental services. The acreage of these important ecosystems has been dramatically reduced by anthropogenic disturbance, and those which remain are increasingly threatened by climate change. In southern California, studies suggest that the historical dominance of the eelgrass Zostera marina may be challenged by the opportunistic competitor Ruppia maritima given predicted environmental changes. To date, limited research has explored how this shift would impact associated biological communities. This study provides preliminary insights into this issue by assessing how structural characteristics and temporal persistence for each species impacted invertebrate communities within an estuarine lagoon in Long Beach, California. Results indicated limited differences in infauna and epifauna communities between seagrass habitats. Patterns were also affected by season, location, and the successional state of sampled beds. Ultimately, differences in the habitat services provided by R. maritima and Z. marina may be most influenced by variance in each species’ temporal persistence, as annual senescence of R. maritima may inhibit development of the complex communities traditionally associated the perennial with Z. marina. This change could have higher-trophic level ramifications and should be considered when planning for future seagrass management strategies in the region.