Increased concentrations of sediments, nitrogen, phosphorous and agricultural chemicals have significant effects on the ecosystems of the inshore Great Barrier Reef close to agricultural areas.

Dissolved inorganic nutrients are quickly removed from seawater by phytoplankton, bacteria and benthic organisms. However, high levels over a long time can create ecological changes across large areas and metabolic changes in most marine plants and animals.

Changes in water quality affect the biodiversity and resilience of reef systems. Higher concentrations of pollutants, such as suspended sediments, nitrogen and phosphorus, indicated by higher levels of chlorophyll and lower water clarity, lead to more algae and less coral diversity. In these conditions, algae take over and reduce the chance for new hard corals to establish and grow.

Increased concentrations of nitrogen in seawater after floods lead to rapid growth of planktonic algae, and can sometimes result in an algal bloom. Algal blooms have the potential to affect other species and the overall functioning of the ecosystem. Crown-of-thorns starfish larvae have a greater chance of survival if their release coincides with an algal bloom.

Increased sediments cause damage to the ecosystem by limiting light penetration, smother coral and other small invertebrates and transport nutrients and pesticides to the Great Barrier Reef. Herbicides can affect the health of marine plants.

Some pollutants have been known to stay in the marine environment for decades and can build up in animals that have high fat contents (e.g. whales and dolphins), are higher on the food web or are long-lived. Pollutants, such as heavy metals, can disrupt reproduction, impair the immune system, and cause neurological disorders and cancers.

Cumulative effects and the timing of exposure to pollutants can magnify the impacts of catchment run-off.