Posidonia oceanica is threatened at depth by mechanical damage from trawling, boat anchoring, and turbidity. Coastal development including shoreline hardening, urban and harbour infrastructure, and sand mining affect the upper limit of Posidonia meadows.

Eutrophication (fertilizer from agriculture and urban waste) and pollution, especially in coastal regions that are heavily populated, is a problem. Fish farm activities and aquaculture affect surrounding Posidonia meadows. Only meadows greater than 800 m away from the fish farms showed no impact from the fish farming activity and meadows up to one km from large fish farms may be affected (Marba et al. 2006). Invasive species also compete for habitat (e.g., seaweeds species such as Caulerpa taxifolia and Caulerpa racemosa). Climate change will be an additional threat through warming of waters (in excess of 28°C) and erosion from sea level rise.

The lack of genetic variability and slow growth makes Posidonia oceanica less resilient to disturbance.