"Tomorrow morning that should be back to showers for a time, but then we've got a southerly change coming through, probably shortly after midday. That will be bringing another risk of thunderstorms."
Thursday's thunderstorm risk was lower, but the thunderstorms would be right over the city, bringing with them a chance for 10-25mm of rain in an hour.
About 6mm was considered heavy rain, so 10-25mm could mean "really heavy, intense rain" for the city, she said.
The most rain the Wellington area had in an hour on Tuesday was 18mm, a reading which came in from a station between Upper and Lower Hutt.
There was a weather watch in place for later on Thursday for both wind and rain, with wind levels possibly rising to severe gales.
Once winds started gusting over 110km/h, Metservice would put out a severe weather warning, rather than a watch.