Dead octopuses, sea cucumbers and other marine life has washed up on South Australia's south coast, not far from the mouth of the River Murray.

Experts are investigating whether the deaths are connected with the high flows from the Murray that have started to cause flooding in the Lower Lakes.

The water off south coast towns near the Murray Mouth has been brown for at least two weeks but what Port Elliot resident and surfer Nisa Schebella described as "carnage" occurred on Thursday.

Hundreds of sea cucumbers and other creatures could be seen dead at Chicken Run, Fisherman Bay and Basham Beach, just east of the main town of Port Elliot.

Sea slugs, seahorses and some fish were also among the casualties.

"It's pretty unpleasant, that's for sure," Ms Schebella said.

Local Jenny Vincent has lived in the area for 40 years.

"We're shocked, we've never seen anything like this before," she said.

"It's just very sad, I think, what's happening to our environment."

Howard McBeth said he comes to the beach every day to walk his dog.

"But in the last eight or nine weeks we've seen a profound change in the biological material that's coming up on the beach," he said.

Mr McBeth said he counted 15 affected species this morning.

"It's absolutely and utterly catastrophic," he said.

Department of Primary Industries and Regions fisheries officers have visited the site to collect samples for diagnostic testing to rule out infectious or notifiable diseases.

"Water samples have also been collected and will be tested to rule out harmful algae and also measure salinity," a spokesman for the department said.

SA Health said there was no evidence of increased microbial contamination, including E. coli, in floodwaters entering Goolwa or nearby beaches.

Deaths could be linked with fresh water

Sea foam has been seen at the Boomer and Knight beaches, west of Port Elliot.

Zoe Doubleday, a marine ecologist with the University of South Australia, said sea foam was often connected with algal blooms.

She said photos of the deaths she had seen looked "macabre".

She said it was an "unusual array of animals" but they appeared to be mostly invertebrates that lived on the bottom of the sea.

"One might be because the animals are going through something like osmotic shock because they're marine animals exposed to more freshwater conditions for a longer period of time, which can cause death.

"A lot of more intertidal animals can cope with changes in salinity, but if it's prolonged and they can't get away from it, perhaps that might be causing them stress.

"If it was a disease, I might find that hard to jump to that conclusion because there's multiple different types of animals impacted."

Swimming lessons continuing

VACSWIM lessons have been continuing as normal in Port Elliot's more protected Horseshoe Bay.

Surf Life Saving SA chief executive Damien Marangon said SA Health had told him the sea foam and brown water was not unsafe for humans.

Alexandrina Council chief executive Nigel Morris said the ocean's water quality was monitored daily.

"We've been assured that it continues to just be organic matter — your leaves, your twigs and so on," he said.

"So it continues to be safe to be swum in, but, yes, it is brown — a chocolatey-milk type of colour — but it continues to be safe."