The dumping of dredge wastes and the discharge of silt from coastal rivers reduces the amount of light available to seagrass communities, thereby limiting their growth. Clearing of land and a variety of other agricultural activities in river catchments can increase the amount of silt washing into the sea, particularly after heavy rains. Trawling by commercial fishing vessels and pollution from urban run-off or ships can also damage seagrass meadows. Many areas of seagrass in the Marine Park have been identified and restrictions on trawling, dredging and spoil dumping implemented. The actual or potential loss of the dugong's seagrass feeding habitat is potentially the most significant issue for the long-term survival prospects of dugongs in the southern Great Barrier Reef.
Dugongs are important in maintaining the health of seagrass meadows.
Seagrass loss was considered a major cause of death of dugongs in Hervey Bay in 1992 following a flood. However, in the Shoalwater Bay area where dugong numbers have declined in recent years, studies since 1995 have shown that there has not been a major loss of seagrass since the 1980s. The Queensland Department of Primary Industries is continuing to monitor seagrass beds in important habitat areas. In the event of a significant die-off of seagrass on the Great Barrier Reef, whether from disease or any other factor, there is no apparent management action which could be taken to redress the situation. Therefore, it is appropriate to minimise the risks to seagrass habitat through the application of best management practices to the possible contributory activities, for example through Landcare programs.