Hundreds of fish have washed up on Hindmarsh Island in South Australia as blackwater continues to move through the River Murray system.

Blackwater has been working its way down the river system since last year's floods, with decomposing organic material, including leaves and bark, washing into the river.

Resident Catharina Taylor said the dead carp had created a "horrible smell" and she feared the smell would get worse in the summer heat.

Ms Taylor said she had alerted Alexandrina Council and the State Government's Primary Industries and Regions SA (PIRSA) department about the dead fish, but was told no help to clean up the mess would be offered at this stage.

"Only thing that I actually heard is that they cannot help, they haven't got the manpower and we should get the community behind us," Ms Taylor said.

"Two [residents] are in their 80s, and four of us are in our 70s, so you know, that's asking a little bit too much.

"And there are also so, so many of them [dead fish], you don't know where to start — if you pick them up, where do you put them?

"We are going to get a horrible smell here."

Council staff monitor situation

Alexandrina Council Mayor Keith Parkes said council staff would monitor the situation, but had not received any complaints about the fish kill.

"We know about the incidents of the blackwater events due to the high river flows and the flooding, so the dead fish are coming down with the flows and we are experiencing high flows in our region now," Cr Parkes said.

"We are probably at about the peak of the floodwaters, so they're managing those flows through the barrages and of course if there are dead fish amongst that, that will go through the barrages into the saltwater side.

"With the wind and the tide they are getting some [fish] washed up along the beach on the foreshore and we have experienced it a couple of times already.

"Over a day or two with tidal action, wind changes and flows — the dead ones get washed out to sea."

Cr Parkes said there was no health risk and council would clean up the dead fish if they did not move naturally.

In a statement, PIRSA said it was aware of the fish kill and it had occurred as a result of the freshwater species being trapped in the saline Coorong waters.

"During these natural kills, it is typical that animals and birds will generally clean up dead fish that remain from these events," it read.

"Dead fish should also decompose rapidly in the current warm conditions and any inconvenience should pass quickly."