The yachts had also been towed back to shore, one at Baleana Bay, and one at Shelly Bay.
MetService duty forecaster Sarah Garlick said wind gusts in the area at the time of the boats capsizing were about 70 to 80km/h.
"That strong wind was probably a factor with those boats."
Garlick said as well as the wind, small hailstones, lightning and thunder were also passing over the capital.
The forecaster said the worst of the stormy front was moving through Upper Hutt early in the afternoon, though many in the city would still be experiencing a fair bit of wind and rain until later in the day.
She expected most of the wet weather to clear from the capital by tomorrow afternoon. Garlick said the wind would ease off this evening and any remaining showers should clear by tomorrow afternoon.
She said a severe thunderstorm watch was also in place for Nelson and Marlborough this afternoon.
Garlick said the area worst affected by the heavy rain and gale force winds was likely to be Marlborough.
She advised those out and about to keep up to date with the latest forecast.