Those gusts would ease off early tomorrow morning, Ms Flynn said.
Weather Watch said the next "burst of showers" would begin soon, and would likely last a few hours.
It said while some downpours may be heavy enough to cause surface or flash flooding, the intense downpours would not be as widespread as they were this morning.
The wet weather was likely to clear overnight for the most part.
Strong winds were also forecast, and while these winds would not be as strong as those this morning, there was still a chance the gusts could cause some damage.
MetService has also issued a weather warning for areas of Wellington and Wairarapa.
Southerlies were expected to develop and rise to severe gale at night, and gusts of 120 km/h were likely.
Snow levels of 300 metres were also expected in Wellington and Wairarapa, which meant there could be some snowfall on Rimutaka Hill Rd overnight.
Large seas and southerly swells are also expected during Sunday and into Monday morning, which may result in coastal damage about the Wellington south coast.
Further south, a cold front was moving across the South Island, with cold southerlies coming behind it. These cold temperatures would cause snow for some areas.
MetService said snow was falling across inland Southland and Fiordland. Light snow showers were expected to continue through the rest of today and tomorrow.
"Tonight is the main risk of the snow. The idea is the snow will be overnight tonight and then tomorrow it will gradually be a bit warmer and it will be fining up a bit too."
Ms Flynn said there had already been some snow in Queenstown earlier today.
Cross winds and limited visibility had effected flights in and out of Queenstown Airport today.
A police spokesman said despite the cool southerly weather it had been a quiet day, with no reports of any weather related incidents.
- NZME