Cyclone Rusty is battering the mining communities of north-western West Australia, floodwaters are peaking again in Queensland, and wet weather is threatening to return to Sydney.

Residents in the Pilbara were on a ''red alert'' on Tuesday night as cyclone Rusty brought winds of up to 120km/h to the north-west of Western Australia.

The Bureau of Meteorology says people in Pilbara region towns between Pardoo and Whim Creek, including Port Hedland and South Hedland, should remain indoors.

Wind gusts of more than 165km/h are predicted in the area as the cyclone approaches the coast, the bureau says. At 2am (WST) this morning, the category 3 storm was barely moving, 125km north-northeast of Port Hedland and 285km northeast of Karratha.

The storm is likely to strengthen to a category 4 and bring major flooding to the De Grey catchment. It is also set to cause significant flooding in the Fortescue catchment and to Pilbara coastal streams, the bureau said.

Rusty's influence is being widely felt as it brings clouds and rain across the continent, reaching Victoria. "It's moisture streaming from Rusty," said Brett Dutschke, senior meteorologist at Weatherzone.

East coast

Combined with moisture coming off the Pacific, "it's the highest humidity we've seen this summer" across the country, Dr Dutschke said.

On the east coast, Gympie residents in south-east Queensland were preparing for their fourth flood in a year. About 34 businesses in Gympie were flooded after the Mary River broke its banks overnight.

Gympie Mayor Ron Dyne was inspecting the damage this morning after the river peaked at 18.44 metres about 2am (AEST).

‘‘It didn’t come up as fast and wasn’t as vicious (as last month’s flood),’’ he told AAP. ‘‘But we’re not breathing a sigh of relief.

‘‘People are just sick of it, we’ve had two floods in a month.’’

Further south, the State Emergency Service continued clean-up efforts across the northern coastal regions of NSW, with 54 communities still isolated after the weekend's wet and wild weather.

Dam spills

Warragamba Dam, Sydney's main water reservoir, is expected to continue to spill as forecasters tip more rain in coming days.

Weatherzone's Dr Dutschke said the dam's catchment was likely to receive at least 50 millimetres of rain between now and early next week, with falls of twice that amount possible.

''Rivers that have had flooding in the past week are likely to get further flooding,'' Dr Dutschke said. ''I wouldn't be surprised if the flooding is a bit worse to what has just occurred and that includes the Warragamba and the Nepean-Hawkesbury areas.''

The bulk of the rain will fall Wednesday and Thursday but showers will continue every day for the next week, adding about 15-30mm over the catchment, Dr Dutschke said.

The extra water, combined with inflows from other tributaries of the Hawkesbury-Nepean, had caused minor flooding to parts of Richmond and Penrith, a spokeswoman for the State Emergency Service said.

While the Hawkesbury-Nepean has not suffered a major flood since 1991, it remains one of Australia's most flood-prone regions, with about 120 floods recorded since European settlement.

Insurers said a major flood could cost billions of dollars because of large-scale residential development in the valley in recent decades.

The weather bureau on Tuesday downgraded the threat of more flooding for the Hawkesbury-Nepean system.

Sydney's wettest days are expected at the weekend before the weather clears up.

With AAP

Weatherzone is owned by Fairfax Media, publisher of this newspaper.