Agricultural soil erosion smothering the GBR with mud.
This section addresses the effect of soil erosion from farms that washes down rivers and into the sea, and potentially onto the GBR. The quantities of mud and sediment involved are very roughly ten times larger than for dredging (see dredging section).
The idea that soil erosion was killing the GBR gained considerable traction during the 1990s and attention was drawn to increased soil erosion from agriculture, perhaps four times as much relative to pre-European settlement. Like the Crown of Thorns Starfish crisis, this hypothesis initially seemed reasonable at first glance and could potentially be supported by graphic aerial and satellite images of apparently muddy water from rivers moving over reefs (see below). More recently, very expensive programs designed to restrict soil erosion on farms and cattle stations have been implemented and, while this work to limit erosion is worthwhile to preserve soil, it is unlikely to have any effect on the Reef.
The ultimate conclusion from this section is that Mud from rivers has effectively no influence on the GBR, where 99 percent of the corals live. It has a very small effect on a few of the Mediocre Fringing Reefs. There is a possibility that water clarity is reduced for months after very large floods and this could reduce the amount of light reaching some of the reefs, although it would appear that most of the GBR is completely unaffected by this possibility.
There are many good reasons to reduce soil erosion on farms on the coast adjacent to the GBR, but this will have no effect on the GBR. It is time to stop blaming farmers for smothering the GBR with mud. There is no mud.
But what about pictures like these?
This second picture of a plume over Old Reef was widely publicised in the media as demonstrating the serious impact of sediment from farms on the reef.  It is a photo from an aeroplane of the same event in the satellite picture above. And there is definitely dirty water over the reef. However, the concentrations of sediment were very low, a few milligrams/litre and most of the brown colour is not from sediment – it is discolouration due to tannins and other organic molecules similar to those that make tea slightly brown (but not cloudy unless you put milk in your tea). If there was lots of mud in the water it would be impossible to see the detail of the reef through the tea-coloured water.
In addition, this picture must be put in perspective as it is a VERY RARE occasion where the river plumes make it to the reef. And this huge flood only managed to reach 3 of the 3000 reefs of the GBR, with extremely low concentrations of sediment, and only for a few days – this reef will probably not see another event like this for another decade. One could take a similar picture for the next 3650 days, and probably just see sparkling blue ocean surrounding a magnificent pristine coral reef.
Proof that this reef is not affected by sediment is that the white coral sand which is clearly visible, has almost no sediment from land. Like all the 3000 reefs of the GBR, the sand here is almost entirely calcium carbonate sands made from broken coral and other organisms that live on the reef.
Far from proving the reef is impacted by sediment, these pictures demonstrate the opposite.
See also sections on
Why you need to geology to understand the reef.
Different types of sediment: how we can tell where sediment comes from and where it goes.
Why waves, not rivers, are the dominant mechanism for making the water muddy along the coast
Why even the small reefs close to the coast and river mouths are not seriously impacted by river sediment.
You will often read that the GBR is being killed by sediment eroding from agriculture. This paper challenges that view. Exposure of inshore corals to suspended sediments due to wave resuspension
 Furnas, M. (2003). Catchments and Corals: Terrestrial runoff to the Great Barrier Reef. Australian Institute of Marine Science, p.334.