MetService says the South Island will bear the brunt of a complex low pressure system which will bring heavy rain to the West Coast over the next three days, from midday on Wednesday.

A cold snap was forecast to bring heavy snow to the Canterbury High Country south of the Rangitata River and north of the stretch between Arrowtown and Ranfurly from 6pm, carrying on through until Friday morning.

State Highway 94 from Te Anau to Milford is closed on Wednesday due to snow. The New Zealand Transport Agency said with heavy rain and high altitude snow forecast, there was an increased avalanche risk.

Rain over the Crown Range Road, linking Queenstown and Wānaka, is also expected to turn to snow on high parts of the road later on Wednesday morning.

MetService meteorologist Braydon White said farmers on the eastern side of the divide of the central South Island - including Mount Cook and potentially Twizel - should prepare livestock for a sudden shift from previously warm conditions to a significant amount of snow above 800 metres with lesser amounts forecast to fall as low as 400 metres.

"Going into a much colder situation in the next couple of days, you'll want to make sure that your livestock are doing okay, making sure you have plans in place if you've got any young lambs starting to appear.”

White said motorists in the area should consider changing their routes to avoid the higher passes and ensure they had snow chains, sleeping bags, warm clothing, and emergency items with them.

"If you do have to travel, maybe consider having a go bag in your car, just in case you get trapped.”

Heavy rain to pelt West Coat 

On the western side of the island, a low pressure system - which was travelling down from the east coast of Australia - could see up to 450mm of rain about the Westland ranges with nearly 200mm expected to fall nearer the coast.

The rain was expected to peak at three points across the coming days - reaching up to 30mm/h on Wednesday afternoon and evening, then again on Thursday evening and in a final burst on Friday morning.

"This fairly complex system is quite wavy and so what happens is you get one wave pushing into the Alps, dumping a whole lot of rain and then it'll ease off for a bit of time as the next wave approaches from the sea,” White said.

"So part of the reason this is such an extended period is because we're capturing two or three waves as they all funnel through.”

White said the drawn-out nature of the rainfall could make the rain across the area a little less severe than the numbers might initially suggest.

"Because it's not all falling in a very short amount of time, that gives time for the rivers to really just get the water away. So while it is quite a bit of rain, if there was anywhere in the country that was going to handle that reasonably well, it would be Westland.

"Certainly there's risk of rivers rising rapidly or slips and potentially road disruption for a time of flooding that could cut places off. But it's hard to be more certain about just how bad it could get.”

Heavy rain watches were also in place for Grey and Buller south of Westport, the headwaters of the Canterbury lakes and rivers about and south of Arthur's Pass, Otago headwaters and Fiordland north of Caswell Sound, White said.

"So while we're expecting the focus of that rain to be the Westland area, the waviness of the system does mean that it moves north and south at times, and so certainly outside of that Westland area we'll still see some decent bursts of heavy rain.

"Alongside that, the north-westerly system will be a bit stronger and that will allow that rain to push over the Alps and into the Canterbury and Otago headwaters as well," White said.

MetService said there was a high chance of the rain watches being upgraded to warnings.