Bushfires, drought and heat are killing some of the region's grey-headed flying fox babies.
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And wildlife carers fear the megabats will continue to perish at an "alarming rate", with predicted heatwaves in the coming weeks.
Wildlife Rescue South Coast bat coordinator Janine Davies has cared for hundreds of bats from the Highlands and Kangaroo Valley in recent weeks.
Ms Davies urged people to call Wildlife Rescue South Coast on 0418 427 214 if they found an injured or distressed bat.
"There's no risk to people if you don't touch them," she said.
"Less than one per cent of the total population may carry Australian Bat Lyssavirus.
"We [the volunteers] all have to be vaccinated."
Native Wildlife Rescue carer Kerstin Schweth said there was not enough food around for the mothers and as a result of this, they abandoned their babies.
"They're falling out of the sky and trees. Lots of mothers and babies didn't make it," Ms Schweth said.
"They're exposed to the elements and therefore they can't cope with the prolonged heat.
"They suffer immensely and they die."
Ms Davies said the importance of the flying fox population could not be underestimated.
"They're our night-time pollinators. If they're not pollinating the forest, there wont be anymore eucalyptus trees," she said.
"The koalas, birds, insects and any species that use those forests will be affected."
Do you want to help carers save flying foxes?
Visit the Shoalhaven Bat Clinic and Sanctuary fundraising website https://giveeasy.org/charity/appeal/shoalhaven-bat-clinic-sanctuary/default? to donate.
