Halophila is the only genus of seagrass lacking basal sheaths on the leaf stems. Like other seagrasses, Halophila engelmannii has rhizomes that run along near the surface of sand or mud, with roots at the nodes to anchor them in place. Each leaf stem grows from a node and has a pair of scales halfway up and another pair at the base of the leaf blades. There are 4 to 8 blades on each stem, each of which is up to 30 millimetres (1.2 in) long and 6 millimetres (0.24 in) wide. Each blade is oval, has 6 to 8 veins and a finely serrated margin.[3]
Flowering occurs in the early summer when the water temperature reaches at least 22 °C. Fragments of the plant that become detached are able to grow into new plants. The seagrass meadow acts as habitat and food source for many invertebrates and fish. In the Indian River Lagoon, animals that feed on Halophila engelmannii include sea turtles, sea urchins, parrotfish, surgeonfish and possibly pinfish.[4] The sea slug Elysia serca preferentially feeds on it by sucking sap.[5]