Overexploitation and influences from activities on land (trawling activities, high hotel density in close proximity to the beach, raking, burying and removing seagrass beach cast material), oil spills and oil pollution, mining, upland clearing, destruction of mangrove forests, dredging, marina developments, eutrophication, siltation, and pollution are all major threats to this species. It is also threatened by unsustainable fishing methods, trawling, illegal fisheries, climate change, sea-level rise and high sediment loads in water.
Destruction of Thalassia hembrichii beds also is caused from cyclones, waves, intense grazing and infestation of fungi and epiphytes, and disease.
Predation by sea urchins is a potential threat.

In Kenyan and Tanzanian shores, overexploitation and influences from activities on land (trawling activities, high hotel density in close proximity to the beach, raking, burying and removing seagrass beach cast material) are of concern. Other localized threats include oil spills, oil pollution, declining water quality due to increasing populations in coastal towns and cities (Green and Short 2003).

In India, the natural causes of destruction are cyclones, waves, intense grazing and infestation of fungi and epiphytes, as well as "die-back" disease. Other threats include anthropogenic activities such as deforestation in the hinterland or mangrove destruction, construction of harbours or jetties, and loading and unloading of construction materials. Anchoring and moving of boats, ships, dredging and discharge of sediments, land filling and untreated sewage disposal also affect this species (Green and Short 2003).

In Eastern Australia, population reduction is caused by increased sediment loads in water, coastal development, dredging and marine developments and damage from boating and shipping activities. Coastal runoff and trawling activities also are of concern (Green and Short 2003).

In Thailand, this species is threatened by a combination of illegal fisheries and fishing practices, and land-based activities, especially mining. Reduced water quality resulting from upland clearing, development along rivers and destruction of mangrove forests are also threats (Green and Short 2003).

In the western Pacific, coastal development, dredging, and marina developments, climate change and associated increases in storm activity, water temperature and/or sea-level rise are of concern (Green and Short 2003).

In Indonesia it is threatened mainly by physical degradation such as mangrove cutting and coral reef damage, and by marine pollution from both land- and marine-based resources. Overexploitation of living marine resources such as fish, molluscs and sea cucumbers is also of concern (Green and Short 2003).

In the Philippines, this species is threatened by eutrophication, siltation, pollution, dredging and unsustainable fishing methods (Green and Short 2003).

In Japan, it is threatened by industrial developments in coastal regions, land reclamation resulting to loss of vegetation, water pollution, disturbance of habitats by fish trawling, and changes in environmental conditions due to human activities (Green and Short 2003).