Seagrass and coral reef habitats are important foraging grounds for species such as green turtles that feed on seagrasses, and hawksbill turtles that feed on coral reef animals. 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 and agricultural activities in a river’s catchment can increase the amount of silt and chemical nutrients and pollutants 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.

Disturbance occurs through noise and direct harassment of marine wildlife, and from increasing vessel traffic, which may displace these species from their preferred habitat. Many areas of seagrass in the Marine Park have been identified and restrictions on trawling and dredge dumping have been implemented in these areas.

A national review by an independent panel of scientists concluded the run-off of sediments from the land into the Great Barrier Reef has greatly increased since European settlement and declining water quality poses a serious threat to the Great Barrier Reef. The increasing run-off of nutrients, pesticides and increasingly fine sediments can smother dugong habitats such as coral reefs and seagrass meadows, cause algal blooms and decrease the amount of light reaching seagrasses, especially after flood events that increase the amount of suspended sediments in the water. Declining water quality may also directly affect marine wildlife by increasing the incidence of disease.

Human activities can destroy or damage beach habitats including nesting sites for marine turtles, for example:

• Coastal developments may totally remove beach sand and restrict access to nesting areas
• Lights from buildings and street lights, can confuse turtle hatchlings, causing them to move inland instead of moving out to sea. Lights can also discourage turtles from coming ashore to nest
• Unrestricted camping and vehicle traffic on beaches can damage turtle nesting areas by compacting the sand, increasing dune erosion and by creating wheel ruts that can trap turtle hatchlings
• Disturbance through noise, direct harassment, inappropriate lighting and increasing vessel traffic may displace turtles from their normal nesting sites.

• The Great Barrier Reef Marine Park Zoning Plan 2003 was introduced to better protect the biodiversity and ecological functions of the Great Barrier Reef ecosystem. Zoning provides protection of the waters around key dugong and turtle foraging sites, including restrictions on access to, and the types of activities that may occur in these areas.
• Critical turtle nesting sites are designated as National Parks or Queensland Marine Parks and are managed by the Queensland Parks and Wildlife Service. The Queensland Parks and Wildlife Office (QPWS) restrict visitor access and use of some of these areas to protect their natural values, including their value as turtle nesting sites
• Many seagrass beds are also protected as Fish Habitat Areas under the Queensland Fisheries Act (1994). These areas allow for multiple use and entry but prohibit activities that may disturb or degrade the seagrass habitat
• In 2003, the Australian and Queensland Governments jointly released a Reef Water Quality Protection Plan (Reef Plan), with the goal to ‘halt and reverse the decline in water quality entering the Reef within ten years’ by reducing the load of pollutants entering the Reef, and protecting and rehabilitating wetlands in the Reef catchments. Regional Natural Resource Management Boards throughout Queensland are working to establish catchment specific water quality targets and address land use practices to reduce the run-off of sediments, nutrients and pesticides. Progress on the Reef Plan’s implementation was reported to the Prime Minister and Queensland Premier in 2005, with a follow up report in 2010. This is being achieved through national programmes such as Landcare, Natural Heritage Trust and National Action Plan for Salinity and Water Quality
• All community sectors are being encouraged to understand the problems of degraded water quality and to get involved in programmes to reduce pollutants entering the Reef and protect and rehabilitate wetlands
• The Great Barrier Reef Marine Park Authority (GBRMPA) has established an innovative educational programme called the Reef Guardian Schools Programme. This programme encourages schools to commit to the protection and conservation of the World Heritage listed Great Barrier Reef. Reef Guardian Schools help to protect the Reef by promoting their ideas, initiatives and activities to communities to encourage all people to “do their bit to look after it!”
• The GBRMPA and Queensland Government agencies are working extensively with local councils and developers to encourage the use of appropriate environmental practices
• A Review of Water Quality Issues Influencing Habitat Quality in Dugong Protection Areas was published in 2002.