Temperatures have cooled across South Australia after a wave of extreme heat but the change has come too late for thousands of animals — including those at a chicken farm and a city bat colony.

Key points: An Adelaide Hills chicken farm lost more than half its flock during the heat

An Adelaide Hills chicken farm lost more than half its flock during the heat Temperatures soared to 46.6C in Adelaide on Thursday

Temperatures soared to 46.6C in Adelaide on Thursday Thousands of bats dropped dead in Adelaide's parklands

Last week the state endured three consecutive days of temperatures in the high 30s and high 40s, which proved too much for flying foxes in Adelaide's parklands.

An Adelaide Hills chicken farm was also devastated by the extreme heat, losing more than half of its flock of 2,000 birds.

Adelaide Hills Pastured Eggs owner Adam Oaten said despite all the measures taken to keep the birds cool, overnight temperatures were just too hot.

"It's a very catastrophic blow to our business. We have customers that rely on us through retail and food outlets so we'll just have to monitor our egg production now and see who we can supply to," he said.

"To replace these girls will take approximately $15,000 but we are trying to do it in stages to get our numbers back up."

On Thursday, Adelaide recorded a top of 46.6 degrees Celsius — topping the previous capital city record of 46.4C set in Melbourne in 2009.

More than 20 locations in South Australia hit record temperatures, with the mercury climbing to 49.5C in Port Augusta.

The farm had 2,000 chickens but that has been cut by more than half. ( Supplied: Adelaide Hills Pastured Eggs )

Mr Oaten said it was not a pleasant task to bury so many chickens, and even his Maremma dog Tom seemed upset.

"We had a delivery of younger chooks only six weeks ago and they were just coming on the lay and unfortunately the heat affected them as well, so it wasn't just older chooks," he said.

"It brought a lot of tears. My partner was in the paddock crying. It wasn't a nice time and I'm tearing up now."

He said he did everything he could to keep the chickens cool.

"We sprayed the ground with water, we've got shade trees, their water is always covered to keep it cool," Mr Oaten said.

"A chook, when she gets hot, will pant, so we use a special additive in their feed that allows them to process protein better and allows them to mitigate against hot conditions much better.

"These animals are more than just a means to an end for us. We love them and we're trying to produce a great product, so it's just devastating that it's happened."

Thousands of dead bats drop from trees

Many of the bats fell from the trees, unable to take the heat. ( ABC News: Carl Saville )

Adelaide's bat colony has flourished in recent years, but was devastated by the heat.

Fauna Rescue SA said while the number of dead bats was still being counted, at least 1,500 grey-headed flying foxes dropped from the trees in Adelaide's Botanic Park, in the parklands and along the banks of the River Torrens.

The organisation's flying fox coordinator Sue Westover said this was the largest number of dead bats she had seen.

"Two days of 40C, followed by a 46C day — we knew it wasn't going to be good," she said.

"We bought a lot of extra spraying equipment so that we could spray the low down ones in the heat to try and give them some fluids.

"By the end of the weekend, we're probably looking at having lost between 2,000 and 3,000 bats."

The number of dead bats is expected to reach up to 3,000. ( Supplied: Sue Westover )

The Environment Department, Botanic Gardens, Adelaide Zoo and Adelaide City Council are also helping to deal with the situation.

Ms Westover said about 100 orphan bats had been brought into care over the past few days.

"All of the deaths have been grey-headed flying foxes, which are actually classed as a vulnerable species now, so this is actually quite devastating," she said.

"They disperse the seeds, and also pollen which creates new tree growth, new forest growth. Basically without the flying foxes helping to spread everything we won't have trees.

"The highest number [of deaths] before we've had was around 600 bats a few years ago in the heatwave."

Bats can carry lyssavirus. People have been urged to keep their distance from them and contact Fauna Rescue SA if they require assistance.