Invertebrate fauna living in seagrass habitats represents a diverse group. Seagrasses provide a rich source of food for invertebrates, primarily in the form of epiphytes.

Epibenthic organisms reside on the surface of the bottom sediments. Some epibenthic invertebrates feed on both the epiphytes living on the seagrass blades as well as the blades themselves, such as the queen conch (Strombus gigas). Other epibenthic species, including the Bahamian starfish (Oreaster reticulatus) and various gastropods, feed on infaunal organisms found living within the sediments. Feeding on detritus, epiphytes, and seagrass blades are various sea urchins that move from nearby reefs to feed in the seagrasses at night. Another echinoderm, the sea cucumber (Holothuria floridana), moves slowly along the surface of the sediments ingesting sand grains and algae. Pink shrimp (Paneaus duorarum) and juvenile spiny lobsters (Panulirus argus) find refuge among the blades of seagrasses.

Epiphytic organisms, dominated by gastropods, are common throughout turtle and shoal grass habitats. These include anemones, bryozoans, and sponges, suspension feeders that live attached to the blades of seagrass. Without the dramatic increase in surface area provided by the seagrasses, the diversity of epiphytic organisms would be much lower.

Throughout shallow turtle grass communities, small patches of stony corals are common. As water depth increases, sponges become more common and may be found growing among the seagrasses or attached to dead coral skeletons.

Although not obvious, infauna communities thrive within the sediments of seagrass beds. The rigid pen shell (Atrina rigida), along with many other bivalve molluscs, is a common filter feeder found within the sediments of many seagrass beds.