There are a number of problems threatening the survival and health of seagrass around the world. As in all ecosystems there are fluctuations in distribution and abundance due too natural causes such as geological and meteorological events (earthquakes and hurricanes) and specific biological interactions. With a growing human population and higher anthropogenic influence the threats to seagrasses have however increased the last hundred years, leading to a world wide decrease in seagrass meadows.

One of the main threats to the seagrass plants is deterioration of the water quality through both pollution and sedimentation. An increased amount of particles in the water reduce the amount of light available to the seagrasses. Pollution in the form of nutrients also promotes algae bloom which furthermore reduces the available light. Eutrophication also leads to an increased biomass of epiphytes and opportunistic macroalgae growing on the leaves of the seagrass. All above mentioned factors decreases the growth of the seagrass and can eventually kill the whole population.

Oil spills are one of the most common forms of chemical pollution of the sea and a potential threat to the seagrass ecosystem. Marine communities situated in the intertidal zone are generally considered most vulnerable to oil spill. Seagrass meadows, which are regularly located in this range, are therefore often negatively affected by these forms of pollution. Studies have shown that in most cases it is not the plant it self that is harmed, but instead the associated fauna, which seems to be more sensitive to toxic chemicals.

Seagrass meadows are also exposed to physical threats in the form of boat propellers, trawlers' nets, and dredging. These are all activities that can damage the leaves, stems and roots of seagrass plants. Seagrass habitats are also often destroyed by reclamation and development of intertidal and coastal areas.

Most of our understanding of seagrass ecosystems is based on local studies, generally in developed nations in Europe and North America. Very little is known about the importance of seagrasses in a global perspective. The lack of information concerning their role in maintaining regional or global biodiversity, productivity and resources, is partly because seagrasses are under-appreciated and their distribution is so poorly documented.

As a result, seagrasses are rarely incorporated specifically into coastal management plans and are vulnerable to degradation. Seagrass ecosystems in the tropics are especially poorly researched, yet it is in these regions that the direct economic and cultural dependence of coastal communities upon marine resources, including seagrasses, tends to be highest.