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Alexandra was hit by heavy rain early in the evening and it also began raining in Queenstown from late afternoon.
The NZTA advised road users to take extra care on State Highways 8 and 85 due to surface flooding.
Fire crews were watching the skies in Wanaka for rain to help them keep control of a big blaze that began on Wednesday afternoon.
Other areas including near Sutton were getting a drenching.
The MetService earlier on Thursday warned of possible flash flooding and issued a thunderstorm watch covering North Otago, Central Otago, Southern Lakes, Dunedin, Clutha, Southland and Canterbury High Country.
The forecaster said the combination of another warm, humid day and light winds would allow scattered heavy showers and thunderstorms to develop over inland parts of the South Island.
About Otago and inland parts of Southland, some thunderstorms were expected to be severe in the afternoon and evening, producing localised downpours of 25-40mm/h.
Rainfall of this intensity could cause flash flooding, especially about low-lying areas such as streams, rivers or narrow valleys, and may also lead to slips.
Driving conditions would also be hazardous, with surface flooding and poor visibility in heavy rain.
The thunderstorm activity was expected to die down late in the evening.
The Ministry of Civil Defence and Emergency Management advised that as storms approached people should:
• Take shelter, preferably indoors away from windows;
• Avoid sheltering under trees, if outside;
• Move cars under cover or away from trees;
• Secure any loose objects around your property;
• Check that drains and gutters are clear;
• Be ready to slow down or stop, if driving.
During and after the storm, people should also:
• Beware of fallen trees and power lines;
• Avoid streams and drains as you may be swept away in flash flooding.