Heavy rain and thunderstorms are expected to hit western parts of the South Island on Thursday.
MetService says a front over the far south is slowly moving northwards.
It says the heaviest falls are expected in Fiordland and Westland from Milford Sound to Fox Glacier.
A further 60mm to 90mm of rain can be expected on top of what has already fallen, especially about the ranges.
MetService is warning that rainfall may surface flooding and slips as well as cause streams and rivers to rise rapidly. Motorists in the area are also being warned that driving conditions may be hazardous.
The warnings are in place until tomorrow morning.
A heavy rain watch is also in place for the remainder of Fiordland north of Doubtful Sound, the remainder of Westland south of Harihari and the Otago headwaters.
Significant smoke drifts over from Australian bushfires
NIWA said much of the smoke will move away from the South Island by tomorrow, although lower concentrations may be observed across the North Island.
Weatherwatch said it was normal for New Zealand to get some smoke from Australia, but that this significant thick wave of smoke was 'almost unprecedented' for New Zealand.
"Smoke is so thick the skies have darkened significantly and people have lights on in the middle of the day," Weatherwatch said.
MetService said fresher air from the Southern Ocean could be expected by tomorrow when southwesterlies were expected to develop at all levels of the troposphere over the lower South Island.