Up to 40 flights due to land or depart out of Sydney were cancelled on Thursday morning as severe weather warnings were issued by the Bureau of Meteorology for heavy falls and thunderstorms across NSW's east coast.
Passengers at Sydney Airport complained on social media of receiving alerts about cancellations at 4.30am, and long queues were seen inside the Sydney terminal.
"In anticipation of bad weather today, domestic airlines advised overnight that some services would be affected," a Sydney Airport spokesman told AAP on Thursday.
Passengers flying in and out of Sydney should check the status of their flights with the airline, the spokesman said.
"Passengers who are travelling today are recommended to arrive two hours prior to domestic flight departures, and three hours for international services," he said.
The cancellations come in the lead-up to Saturday's AFL Grand Final, with Victorian travellers enjoying two consecutive public holidays before the weekend.
Queensland is also on school holidays, while the NSW, Northern Territory, ACT and West Australian term ends on Friday. Tasmania and Victoria go on holidays at the end of next week.
It is expected 2.4 million people will fly through Sydney during the holiday peak, a Sydney Airport spokesman said.
Meanwhile in the Sunshine State, operations are "flowing relatively smoothly" at the Gold Coast airport, according to a spokesman.
The spokesman told AAP operations are being assisted by an ambassador program that is helping people board their flights and check in at the terminal.