Parts of the South Island can expect to get a drenching today.

MetService has heavy rain warnings in place for Fiordland and around the headwaters of the Otago Lakes.

A heavy rain watch is in place for the headwaters of the Canterbury lakes and rivers, with rainfall set to exceed warning criteria within 20km east of the main divide.

A rain watch further up the West Coast starting from Wednesday nightwill last through to the early hours of Friday.

Meteorologist Karl Loots told Morning Report people in Fiordland north of Doubtful Sound could expect the rain to start from Wednesday morning with as much as 250mm to 350mm on the way over the next 30 hours.

"This is very heavy significant heavy rain even for parts of the country that are quite accustomed to heavy rain."

For the headwaters of the Otago lakes and rivers a heavy rain warning is in place with the heaviest rainfall forecast for Thursday morning.

As much as 250mm could be expected near the Divide, he said.

It was a warm system for this time of year and it would be fed by snow melt, Loots said.

Rivers were still running high with eastern Otago affected by flooding in some parts a few weeks ago.

Two factors made it significant.

"It's a very warm air mass being driven from the sub-tropics down to the southern parts of the South Island and then secondly, this front is moving extremely slowly so it would be a very prolonged period of rainfall."

It could last from 24 to 30 hours for many areas and could spread up the West Coast and it was likely the watches would be upgraded to warnings.