"Today should be more straightforward, however a number of passengers who weren't supposed to be in Melbourne are here this morning," the spokesman told news.com.au.
"So there will be a bit of recovery effort today as airlines rebook passengers, which we will help streamline."
The spokesman said conditions had significantly eased after parts of the state received an "enormous amount of rain" overnight.
"It's still raining in parts of the city, which is helping with smoke and air quality around the airport today," the spokesman said.
While about 30 Virgin Australia flights were cancelled on Wednesday as a result of weather conditions, there were no big disruptions for passengers early on Thursday.
On Thursday, NSW will receive much-needed rain in parts of the state that haven't experienced heavy falls for months.
Most of the state is expected to receive rain, except for the west and southwest, with the falls to continue into Monday.
Areas around the south coast and Southern Tablelands are predicted to receive up to 30mm, but the Bureau of Meteorology says the rain will be patchy and exact falls are difficult to predict. However, Sydney will receive intense falls today.