People have been warned to watch out for rising lakes and rivers, and keep off Southland roads, as wintry weather hits the South Island tonight.

Heavy rain and thunderstorms were forecast for the West Coast and Southern Alps, with up to 200mm of rain expected in the Westland ranges between this afternoon and tomorrow morning, the MetService said.

Many roads near the lower reaches of Southland rivers had been hit by flooding, and State Highway 99 between Invercargill and Riverton closed late this afternoon.

People were strongly recommended to avoid unnecessary travel tonight while rivers peaked, as water could flood roads , Southland District Council asset manager roading Russell Hawkes said.

"Our maintenance contractors are out monitoring the situation and are endeavouring to put warning signs on the worst-hit roads, but please be careful and drive to the conditions if you are travelling on roads around the district," Mr Hawkes said.

Heavy rain was also expected to reach the headwaters of Otago and Canterbury lakes and rivers.

Lake Wakatipu in Central Otago was about 1m below the first flood warning level, and nearby Lake Wanaka was just over 2m below it.

"With MetService currently predicting heavy rainfall over the next few days, along with snow at higher attitudes, lake levels could rise significantly," Otago Regional Council spokesman Dr John Threlfall said.

The Clutha River was also likely to rise rapidly over the weekend and remain high for several days, he said.

A further 200mm to 300mm of rain was expected in the Fiordland and Westland ranges over the weekend.

"Trampers and mountaineers are advised that with both fronts, conditions in South Island mountain areas are likely to be extreme with severe gales, heavy rain and thunderstorms," MetService forecaster Oliver Druce said.

Snow was expected on the highest parts of the Milford Road tomorrow morning before turning to rain again by midday, MetService said.