Image caption The giant potato cod is among thousands of species sitting in the path of the Queensland flood water

As flood waters in the Queensland capital Brisbane begin to recede, scientists are casting their eyes out to sea and wondering whether the region's greatest natural feature, the Great Barrier Reef, will be scarred by the experience.

This is the world's largest reef system - in fact, the largest thing on Earth made by living organisms, stretching for 2,600km along the coast.

Its myriad of islands and tendrils teem with fish, also supporting dugongs, dolphins, turtles and shellfish - and because of all that, a tourist trade worth several billion dollars per year.

The flood waters emerging from Brisbane itself are not a major concern, as the reef lies further north.

But northern rivers are also seeing flow rates way above normal.

As the water floods into the seas west of the reef, it inevitably freshens the environment around the reef; which is not good news.

"Freshwater kills corals, and there is nothing we can do about it," says Katharina Fabricius, principal research scientist with the Australian Institute of Marine Science.

Queensland is a heavily agricultural state. And this means that the flood water brings with it another threat.

Pesticides, herbicides, fertilisers and sediment - mud - are washed off the farms, into the rivers and then onto the reef.

Image caption Flood water, with its cargo of mud and nutrients, is pouring into the sea from the Fitzroy and other rivers

The fertilisers do in the sea what they do on land - stimulate the growth of plants.

But here, that is a problem, as the marine plants cover growing coral, choking it to death.

The sediment also hurts the reef, blocking sunlight and covering the coral fronds.

This run-off degrades the reef at the best of times; but in flood conditions, it becomes much more serious.

"The young corals are highly sensitive to exposure to organically enriched sediments," Dr Fabricius tells BBC News.

"That retards the ability of reefs to recover from the freshwater damage.

"My own research has also shown that increasing levels of nutrients can lead to more seaweed - up to a five-fold increase - and reduce coral biodiversity, with half of the coral species potentially lost from the exposed sites."

Local issue

The sites at highest risk are reefs close to the shore and close to the mouths of rivers discharging flood water.

We're very spoiled here in terms of the amount of coral and the speed at which it can grow and recover Dr Alison Jones, CQ University

For example, the Keppel group of islands lies about 10km from the shore, in the path of water rushing from the mouth of the Fitzroy River.

Scientists monitoring coral there say they have already seen indications of coral damage, but that is is too early to tell how big the impact is likely to be.

As the flood water spreads further from land, it dissipates in the seas - but can still have major consequences.

"The waters discharging from the Fitzroy River are moving hundreds of kilometres north and 50-100km offshore," says Michelle Devlin, a coral reef ecologist from James Cook University in Townsville.

"There is the potential for large areas of the reef to experience river plume water, with potentially damaging levels of nutrients, sediments and pesticides."

Recovery hopes

On their own, the floods would not necessarily be a significant threat.

The region has had them regularly down the years. 1991 saw major damage to inshore coral - but it recovered.

"The 1991 flood was extremely hard for the reef - pretty much most of the corals were wiped out down to about six to eight metres of depth, and it took about 10 years for them to recover," says Alison Jones from Central Queensland University in Rockhampton, through which the Fitzroy flows.

Image caption The crown-of-thorns is a voracious coral predator

"But they recovered magnificently; we're very spoiled here in terms of the amount of coral and the speed at which it can grow and recover."

However, what concerns scientists most is that this is just one more hit for an ecosystem that is already struggling to cope with many long-term threats.

These include overfishing, climate change, disease, chronic pollution and shipping.

"The problem is that all forms of disturbances, loads of sediments/nutrients/pesticides, as well as bleaching events from warming seawaters, more intense cyclones and more frequent outbreaks of coral predators such as the crown-of-thorns starfish, all increase in frequency and intensity," says Katharine Fabricius.

"This gives the reefs often not enough time to recover before they get hit again."

The crown-of-thorns starfish is a good example of how the various threats interact.

It eats coral polyps, the organisms that actually build reefs.

Overfishing of one of its few predators, the giant triton, allows the starfish population to expand. Meanwhile, in at least one reef system, fertiliser run-off has stimulated the growth of algae, which has provided predators with an alternative food.

Reefs stressed by climatic factors, pollution and disease will be less resilient to attack by the voracious starfish.

Climate of concern

It is likely to be several weeks at least before scientists are able to gauge the true scale of the flood's short-term impacts.

The continuing threat of bad weather means that travel to the reef is constrained.

And it will be some time - the exact period dependend again on weather - before all of the flood's cargo has travelled through the multifarious fronds of the reef system.

The hope is that it will prove to be a one-off hit from which corals, fish and everything else can recover.

The long-term threats, though, remain, despite recent initiatives to reduce agricultural run-off, constrain shipping and fishing, and tackle the crown-of-thorns.

Climate change is likely to hit reefs in the middle of the tropics harder and faster than the Great Barrier Reef.

Neverless, along with ocean acidification also caused by carbon dioxide emissions, it remains the most significant issue for the region, with a 2007 report by the Great Barrier Reef Marine Park Authority concluding:

"Projections of future sea temperatures suggest that coral bleaching could become an annual phenomenon in the course of this century, threatening to undermine the physical and ecological foundations of this diverse and productive ecosystem."