The women, said to be aged in their 40s, had come prepared to brave the waters – with helmets and life jackets – Constable Chris Hill, of the Warrandyte Station, told Fairfax Media. "But the water was too strong for them."

As they made their way down the river, their kayak snagged on something, he said. They flipped out of the boat and caught hold of a tree, as the kayak made its way another 20 or 30 metres downstream.

They held tight as two friends who had decided not to enter the water sought help.

First responders received a call shortly before 11am notifying them of the incident, and launched a combined rescue effort that included Victoria Police, State Emergency Service and Melbourne Fire Brigade.

Initially, two boats were taken up the river in an attempt to rescue them, said Constable Hill, but the water was too shallow, "so [the women] had to jump into the water".

They were successfully rescued from the river about two hours after they fell in.

A flood warning has since been issued for the Yarra River catchment and a thunderstorm is forecast for the central region of Victoria, which includes Warrandyte.

Friday's incident came less than 24 hours after a man and his dog were rescued from floodwaters in Yarrawonga, in Victoria's north-east.

State Emergency Service incident controller Keith O'Brien said the need to rescue the man should serve as a reminder not to enter floodwaters under any circumstances.

"The rivers are floodwaters at the moment and the message that people should not drive, walk or play in floods needs to get out there," Mr O'Brien said.

"Kayaking, boating in flood waters is not a good idea," he said.