I was shocked when I opened the contents of the link I provide:

It the latest news on the annihilation of the environment in the Gladstone Region in Qld.

http://www.abc.net.au/news/2011-11-09/gladstone-harbour-in-pictures-and-quotes/3650296

Is this sort of thing the beginning of the end ?.

No, it's not the beginning of the end - it's nature doing its thing.

The run-off due to the huge rains over the last year will have carried all sorts of minerals into the ocean. Clearance/farming may have contributed by allowing more scouring of soils. The dredging will churn stuff up, but that will be a very local event, compared with the regional effect.

How to test? You'd look at the questions:
1. How widespread is the effect on fish?
2. Is it worse in estuaries where material in run-off tends to hang around rather than being washed out to sea, to settle further out on the continental shelf?
3. Is the suite of minerals similar to the area being dredged or from further afield?
4. Are there historic examples following exceptional rains, before dredging/development?

The study should cover those aspects and others; it will be interesting to see the results.

PS In the Murray-Darling there is a natural phenomena called black water, which kills lots of fish after heavy rain. There's an Aboriginal account that fish fled ahead of flood waters (and were easy to trap) because they didn't like the taste of the water.

Black water in the murray darling is rotting vegitation and gum leaves washed back into the river after floods, which causes a lack of oxygen, this kills fish, and crayfish take to land to find more suitable water. Only flushing fixes the problem. I have never seen fish with visable wounds caused by any sort of water. Or would that be caused after death.

Yes thinker 2 this is not the end.
But it is a concern ,we see in the post between us the truth.
For a very long time farm run off and yes storm water, has seen such , and massive deaths of marine life.
All over Australia.
And we should do something about it.
Storm water is the streets rubbish disposal unit.
We still dump sewage in it some times untreated.
Farmers, some still, use a bit too much just in case, and do not try to control run off, its just a little bit they tell them selves.
It is said 60% of the jobs children starting school now will do, have not yet been invented.
One should be keeping creeks rivers and streams clean, and stopping pollution getting away.
Another? future conservationists must take control, clean up after, the black stupidity of some, who by their actions make the word green or conservation dirty in most minds.

579 red rot, one of many names for such open wounds on living fish as in this case.
Happens from the very south to the very north of the east coast.
Regularly.
Even more in lakes and rivers bays and harbors.
I have seen hundreds of ton of dead or dieing fish too with this mark.
Floods do indeed kill fish.

floods are a great time for miners [drillers/even farmers
to dump bad polution waters..into the flood waters

by accident or design
dont understimate the chemical affect

govt knows that will kill the reef..;kill industry..
yet persists on gifting our wealth to multinationals..
[and hang the real cost][or the public debt]