This can be due to a number of things and most likely due to the synergistic effects of multiple factors.
As Rory said, with this type of flooding, everything that have settled to the bottom over time will be churned up back into suspension. Added to this is all the muck resulting from surface run-off caused by the high rainfall. This will also include a variety substances that can be toxic to fish.
The number of suspended particles in the water is another big problem for any gill-breathing organism in the water. These particles will get caught up in the fine mesh that makes up gills, thereby significantly reducing the surface area available for gas exchange and thus breathing. under normal conditions this also happens, but fish can generally clear the gills with a "coughing" motion that forces more water the gills at a higher rate, dislodging particles stuck in the gills. One of the theories of why fish jump is that they may use the jump to force water and bubbles through the gills to get rid of irritants.
Another possible factor is that with the water movement, sediment upwelling and run-off, the concentration of dissolved substances in the water will increase. Basic water chemistry will tell you that the more dissolved substances you have in the water, the less oxygen will dissolve in the water. Thus, the oxygen concentration in the water will be less than under normal conditions, even with heavy aeration of the water, the dissolved substances will prevent more oxygen from dissolving into the water.
Now for the synergistic effects on the fish....... Imagine a fish in the flooded river.... you must swim much harder than normal due to the speed of the current, and you are constantly bombarded with all kinds of hard and nasty objects coming at you at high speed, and you cant see them coming because of the dirty water and your general poor eyesight. Thus you are working much harder to just keep your position in the water, never mind getting out of trouble, so you are breathing much harder. Apart from your muscles screaming for more oxygen, and you breathing as fast as you can, you suddenly find that there is too little oxygen in the water, and there are also a number of substances in the water that makes you feel sick and weak. On top of that your gills are being packed full of fine particles, and a cough only helps for a second or two.... You finally manage to get into a quite patch out of the main stream, where you can try and re-recuperate, but you find that millions of others have the same idea and soon the "save-haven" is over crowded and with every breath you breath in more and more waste products produced by the same bunch around you that are sucking up the last bit of oxygen in the pool.............and then you pass out, never to awaken again...