A severe weather warning has been issued for parts of NSW, with damaging wind gusts of up to 90km/h expected to wreak havoc on trees and powerlines.

The Bureau of Meteorology issued the severe weather alert for the Snowy Mountains and parts of the NSW South Coast and the Southern Tablelands on Thursday.

The winds are brought by a low pressure trough, which is moving through parts of NSW and the ACT and also brings the potential for severe thunderstorms.

Sydney, the Illawarra and Central Coast won’t miss out, with mid-afternoon storms forecast there as well.

Meteorologist David Wilke said anywhere south of the mid-north coast should be prepared for bad weather.

“Wind gusts really are the main concern today for anywhere along the coast south of about Port Macquarie, and then also the central tablelands, southern ranges and parts of the inland north,” he said.

“At this stage hail is looking reasonably unlikely, just because of how fast the storms are moving (but) it’s not out of the question. It’s something we’ll be monitoring through the day.”

Tweet from @BOM_NSW

Victoria’s east and Tasmania are also in the path of the wild weather. Damaging winds with gusts up to 100km/h are likely in Victoria’s eastern alpine areas while the system hit Tasmania in the morning, bringing rain and gusty winds.

Up to 90 millimetres of rain is expected in the island state’s north and higher falls are possible in elevated areas.

By early Thursday, Flinders Island had already had 16 millimetres of rain and 25 millimetres had fallen on King Island.

Emergency crews were on alert in the state’s north, with soil already damp from recent rain.

“These winds will likely cause trees and tree limbs to fall,” SES regional manager Mhairi Revie said.

Tweet from @VICSESChief

The blast of wild weather comes after the giant low-pressure system stretching from Darwin to southern Australia brought heavy rain to parts of Victoria and southern NSW on Wednesday and overnight.

Warrnambool, in Victoria’s south-west, was hardest hit. It had 56 millimetres of rain in the 24 hours to 9am Thursday. Nearby, Port Fairy got 47 millimetres and Casterton 34 millimetres.

Port Fairy SES controller Steve McDowall said crews had been desperately trying to save houses in Koroit and Allansford, where there was most concern.

“[We’re] seeing houses being impacted by floodwater this morning,” he told the ABC.

“I know crews across Warrnambool and Port Fairy are working very hard at the moment in trying to save several properties from going under water.”

Mr McDowall said the SES was also sandbagging homes.

Senior forecaster Kevin Parkyn said the system heralded the onset of the La Nina weather pattern, which will deliver a wetter summer.

“The atmospheric conditions are just ripe for that system to intensify tonight right over Victoria,” he said.

“We call that process cyclone genesis. This system is linked to tropical moisture, we haven’t seen that for quite some time.”

-with AAP