Victoria's Deputy Premier Peter Ryan on Monday said overall he is satisfied with the stormwater and emergency management systems, which have been dealing with the weekend flooding across the Australia's state.

Victoria's southeast, including suburban Melbourne, was hit hard by a massive rainfall on Friday and Saturday, while other parts of the state still reeling from recent record floods were also impacted.

Victoria's 5.8 billion U.S. dollars desalination plant, which is under construction at Wonthaggi, was damaged by the floodwater during the weekend.

Ryan said the extent of damage to the plant and throughout the state was still being assessed.

"We will need to assess the contract terms and their relationship with this damage, whatever it is," he told Australia Associated Press in Melbourne on Monday.

"The extent of it is yet to be established. They are matters that are under discussion at the present time."

However, he believed that overall storm water and emergency management systems had worked well.

Some parts of the state received 100 to 150 millimeters in just a few hours on Friday night, causing severe flash flooding which was compounded by further rain on Saturday.

The torrential rain swamped railway stations, major roadways and suburbs in Melbourne's southeast, prompting 6,300 calls for help to the State Emergency Service (SES).

Almost 120 rescues had to be carried out, 80 from cars where people had attempted to drive through floodwaters.

Ryan said he believed the state's storm water system was adequate.

"You couldn't build a system that would be able to handle that (the weekend deluge)," he said.

The SES said the weekend flooding is starting to either recede or ease significantly, but a close watch was being kept on river levels, with flood warnings in place for a number of rivers.