Two women, aged 53 and 31, were arrested on arrival at Melbourne airport on Thursday by counter-terrorism officers, the Australian Federal Police said.
A third woman, aged 32, was arrested upon arriving at Sydney airport.
A total of four women and nine children arrived in Sydney and Melbourne on Thursday evening after years spent in a Syrian refugee camp.
The 14-hour Qatar Airways flight to Melbourne from Doha landed about 5.30pm following a short delay.
Passengers were greeted by a strong media contingent, with reporters and television cameras gathered in the international arrivals hall.
A group of men dressed in black also seemingly waited for the Melbourne contingent to appear but did not answer questions from reporters.
One man, who was on the same plane as the women from Doha, said he did not notice any disturbances during the flight.
Asked about the women, he said he had only read about them on Instagram.
"We are not ISIS brides," one woman said after arriving on an earlier flight from Christchurch.
"What famous person is coming? Maybe I need to hang around," one man said.
Meanwhile, the one "bride" who arrived in Sydney was escorted off the plane by uniformed officers before any other passengers were allowed to leave, people arriving at Sydney Airport told reporters.
She was arrested and taken to Mascot Police Station, an AFP spokesperson said.
Many of those arriving on the Qatar Airways flight to Sydney did not know why they were being welcomed by such a large media pack but reported seeing uniformed officers outside the plane when it landed.
The pilot made an announcement after landing asking people to stay in their seats and the plane was stopped for about 10 minutes before anyone was able to leave, one passenger told AAP.
"Who's on the plane?" Sathvik Chatakondu said.
While the women face the prospect of lengthy legal proceedings, uncertainty still surrounds how the children will be integrated into a completely alien society.
Some women travelled willingly to support their partners who wanted to fight for Islamic State, but advocates for the group say others were trafficked or only went to the Middle East to keep their family together.
All children in the group of 13 returning home would likely need help integrating into Australian society after years in Syrian camps, while others could need more intensive de-radicalisation support, leading extremism researcher Michele Grossman told AAP.
"This is going to be very much case by case," the Deakin University professor said.
"We can't make assumptions that all children will respond equally ... to the kinds of indoctrination activities that we know have gone on in those camps."
Support from the community would be crucial to help them recover from years of trauma, Prof Grossman said.
"If the community is only ever going to turn them away and refuse to have anything to do with them ... then what hope are you giving them, and what prospects are you offering them?" she said.
The group of women and children are all Australian citizens and government ministers have said there are no measures that can stop their return.
The premiers of both NSW and Victoria said the children returning to their states would undertake deradicalisation programs and the safety of their communities was paramount.
One woman has been barred from entering Australia on national security grounds and the opposition has reiterated its calls for the entire group to be blocked.
The group forms part of a larger cohort of about 30 women and children who have been trying to return from Syria for years after the 2019 toppling of Islamic State.
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