Halophila stipulacea is a dioecious perennial herbaceous plant with a terete rhizome and erect stems that reach up to 2-3 x 0.5 mm long. Leaves are of 1 pair on each erect stem; the blade is 2.5-5.5 x 0.6-1 cm, glabrous, oblong-linear, with rounded apex, cuneate base and serrulate margins. Male flowers are with 7–15 mm long pedicel and ovate tepals, with a prominent central vein; while female flowers are sessile. The fruit is ellipsoid, with a beak up to 6 mm long and 30–40 seeds.