Natural factors play a small role in the dilapidation of the Great Barrier Reef for it is the human existence which threatens this "rainforest of the sea" (McCoy, 2001). As a result, the Reef suffers from litter and fuel pollution, disturbance of fauna by reef walking, snorkelling, diving and anchors, and the decrease of various species from over-fishing. However, the most critical concern is the deterioration of water quality in the past 75 years. Both marine and land-base activities contribute to the increasing levels of nutrients and sediment in the reef ecosystem. Insensitive land development plays a major role in providing nutrient run-off from both urban and rural areas, into the Barrier Reef. Sugar cane farming and cattle grazing can often use pesticides, fertilisers and many other chemicals, which infiltrate the sea during heavy rainfall periods. Furthermore, domestic sewage waste is discharged into the ocean, containing substantial amounts of damaging nutrients. However, local policies have been implemented which ensures solids from sewage is removed and the remaining substance is chlorinated. Nutrients are produced for terrestrial purposes and therefore only disrupt the natural marine processes, often leaving irreversible damage. .
High levels of nutrients particularly nitrogen and phosphorus, can cause eutrophication, which increases porosity of the corals. The increased porosity can weaken the skeletons of coral and reduce the protective strength of the reefs, making them more prone to damage from storm action. Plankton and the attached algae compete with coral for light and nutrients but high levels of nitrogen can increase planktonic algae, pressuring the coral for settlement space and increasing sedimentation. .
An additional concern for water quality is the amount of sedimentation that is carried into the coastal marine ecosystem, altering the water clarity. Cyclones are often accompanied with strong floods that can cause a fierce outflow from rivers carrying sediment and vegetation into the Great Barrier Reef Lagoon.
