The high primary production of the seagrasses (seagrass and epiphytic and benthic algae) and the three-dimensional structure of the vegetation are characteristics that a number of different animals, both in the seagrass ecosystem and in adjacent habitats finds attractive. A number of different animals move between the different ecosystems, utilizing different resources and services in the different habitat. These migrating animals are mobile links, which connect the seagrass meadows with other ecosystems (mangrove, estuaries, coral reef, open ocean) in the seascape.

The fishes of the seagrass meadow can be divided into four categories:

(1) Permanent residents, species that stay throughout their life in the seagrass habitat. They are typically small in size and cryptic. Common year-round resident fish include the pipefishes (Syngnatus spp.), seahorses (Hippocampus spp.), and the inshore lizardfish (Synodus foetens). An important grazer in tropical seagrasses is the "seagrass parrot fish" Leptoscarus vaigiensis.

(2) Temporary residents, species that are only seasonally or during a part of their life cycle present in the meadows. The spotted seatrout (Cynoscion nebulosus) and silver perch (Bairdiella chrysura) are seasonal residents that are common as juveniles in seagrasses.

(3) Regular visitors, species that frequently visit the meadows (e.g. fishes that migrate on a diurnal basis from coral reefs), for example grunts and gray snappers (Lutjanus griseus). Both species live diurnally on the coral reef and feed nocturnally over seagrass beds. Snappers in general (e.g. Lutjanidae) are important visitors of seagrass ecosystems.

(4) Occasional visitors, fishes that visit the beds only now and then. Nurse sharks (Ginglymostoma cirratum), smalltooth sawfishes (Pristis pectinata), and different species of sting rays are all examples of species that visit seagrass habitats in search of prey from time to time.

In areas were the seagrass meadows are situated adjacent to coral reefs, fish show diurnal migrations from the reefs to forage over the seagrass beds. In many examples food is the most important attraction. But it is not the only factor attracting the fishes. For some species the refuge function of the seagrass canopy is likely to be the main reason. A number of studies have shown that the predation risk to invertebrates and fish is smaller when they reside in the canopy of seagrasses.

Apart from functioning as forage and refuge area, the seagrass beds also serve as nursery habitats for many fishes. Spawning of these species usually does not occur within the beds, but takes place elsewhere, e.g. in the coastal ocean. Settlement into the seagrass follows after a pelagic larval phase, and the juveniles only remain in the meadows for a certain time (several weeks or months). Among the number of fish species that may spend part of their juvenile existence in the seagrass beds are several species important in recreational and commercial fisheries.

The seagrass meadows do not only function as a nursery ground for reef and oceanic species, but also juveniles of mangrove fishes are encountered in the beds. Seagrasses in East Africa are the major contributors to adult fish populations in coral reefs.

Although seagrass meadows are important as nursery habitats, it is not an exclusive feature for the habitat. A number of studies have shown that juveniles known to occur in seagrass beds may also use alternative nursery habitats, such as algae areas, oyster rocks or even bare sediments.

Many decapod crustaceans use the seagrass meadows as nursery habitat, just like the fishes do. Some decapods may be found up to the adult phase, but frequently the seagrasses are used as a nursery habitat by post-larvae and juveniles only. One example of a commercially important species that can be encountered in the beds is tiger prawns, which juveniles are predominantly found in seagrass meadows.

Turtles

Of all the sea turtles in the world the green turtle ( Chelonia mydas ) is the only one primarily living on macrophyte food. After leaving the nesting beaches the turtle spends the first years of its life as an omnivore in the open ocean. When the turtles have reached a size of 25-35 cm, they leave the pelagic habitat and enter benthic foraging areas. The turtles feed primarily on seagrasses, algae being the principal food where seagrass meadows are lacking.