The search for a three-month-old baby boy still missing after the bodies of his mother and sister were recovered from waters off SA’s South East has been suspended because of weather conditions, police say.

Police said it was too dangerous to continue the search off Port MacDonnell, and it was halted about 3:30pm on Tuesday but that it would resume tomorrow morning.

Superintendent Trent Cox, officer in charge of the Limestone Coast Region, said while police held grave concerns, they would leave “no stone unturned”.

“The information we have from survivability experts is that it is very, very unlikely the missing baby has survived,” he said.

“[But] we will continue to search until the expert advice tells us that there is no prospect of finding the child alive.”

Cliffs at Cape Northumberland, near Port MacDonnell in South Australia's South East.

Emergency services have searched the area for a second day. (ABC News: Guido Salazar)

The girl who died was 23 months old, while their mother was a 36-year-old from Compton, near Mount Gambier.

Their bodies were recovered on Monday.

“We are keeping a very open mind as to the circumstances that led to the mother and daughter being in the water, and the other child being missing,” Superintendent Cox said.

“There are a number of scenarios we’re investigating.”

Police said today’s weather conditions had been challenging, and that high winds had meant the search was confined to land.

“[Conditions] did not enable us to get water assets on the water,” Superintendent Cox said.

Earlier, authorities said the missing boy was “about” two months old, and Superintendent Cox later described him as a three-month-old.

Police investigating ‘number of theories’

The tragedy first came to light about 11:15am on Monday, when emergency services were called to Cape Northumberland, a headland near Port MacDonnell distinguished by rugged cliffs.

Police said the woman’s car — a white Isuzu MU-X, with South Australian registration S592 BJR — was found “abandoned with its engine running”.

They said there was “no information to suggest” anyone else was involved in the incident.

SA Premier Peter Malinauskas today sounded a note of caution, warning that there was a need to be “careful not to jump to conclusions”.

“It’s very difficult at this point in time to understand exactly what transpired here,” Mr Malinauskas said.

“There are a number of theories that the police are actively investigating.”

Cliffs at Cape Northumberland, near Port MacDonnell in South Australia's South East.

The area is characterised by its rough conditions. (ABC News: Guido Salazar)

Police have asked anyone with information about the woman’s car, or with dash cam footage that could assist, to contact them.

The search and investigation has involved SES volunteers, SA Police’s Water Operations Unit, Major Crime investigators, the Forensic Response Section and other maritime agencies.

Superintendent Cox said weather conditions were expected to be more favourable on Wednesday.

“The forecast is that it’s not as extreme as today — still challenging. It’s an exposed area,” he said.

“We’ll be out there at first light again, we’ll hold a briefing for our emergency services personnel and volunteers who are assisting, as well as the police.”

The search was expected to resume about 8am.