An increase in the number of dead fish washing up on the banks of the River Murray is due to flood waters making their way down from Queensland and New South Wales, according to The Department of Primary Industries and Regions (PIRSA).

A PIRSA official says while the event is natural, locals should expect to see more of these fish kills over the next month as the effects of the La Nina weather event continue to be felt.

Fleurieu locals have reported seeing large numbers of dead fish at Milang, upstream of Lake Alexandrina and at Clayton and Goolwa.

The fish have included young carp and native fish such as bony bream.

Brad Page, the Principal Biosecurity Officer with PIRSA told the ABC this week they have ruled out infectious disease and chemical contamination as the cause of the fish deaths.

He says flood waters had increased the salt levels in the water by as much as 50 per cent from levels recorded only a few months ago.

Due to the man-made system of locks, barrages and weirs along river, the salt takes longer to flush out of the system then it would do naturally.

He says the high flows in the system have also stirred up sediment and this has also put more pressure on fish who are already finding it harder to take in oxygen through water with an increased salt load.

“It’s an environment fish kill,” he says. “It’s a natural event.”

“It’s just the culmination of their river environment changing so dramatically, it’s not what they’re used to.

“These are fish that would prefer to live in a warmer environment and all of a sudden they’re being impacted by these tremendous flows of water.

"So, while we’ve got these La Nina weather events, PIRSA is actually expecting more fish kills to happen – particularly in the next month – while we’ve got these high flows continuing to flush salt and sediments and continuing through this cold winter, well what feels like winter, but early spring.”