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About 50mm to 60mm fell in the headwaters of Lake Wanaka yesterday and the Otago Regional Council predicted it would again rise, exceeding its first alarm level of 279.4m in the early hours of today.
Council duty flood officer Phillip Purves said it was not expected to rise high enough to cause flooding in the township but the council would monitor the situation overnight.
"We're fairly confident we are not looking at flooding."
Much less rain had fallen in the headwaters of Lake Wakatipu, so its level was not expected to increase significantly from its 2pm yesterday level of 310.864m, which was just above its first alert of 310.800m, he said.
"The worst is over."
Wanaka and Queenstown townships received only about 10mm to 12mm from the front, compared to 84mm at Franz Joseph and 62mm at Mt Cook.
Dunedin received 4mm.
The "good news" was that while a quick southerly change today would cool temperatures, ease the humidity and bring a few showers, a high was building that was expected to bring settled weather through to the middle of next week, he said.
Queenstown Lakes District Council communications officer Jo Blick said monitoring staff had liaised with retailers in Wanaka and it was unlikely any would be affected by flooding.
Queenstown Lakes deputy mayor Lyal Cocks, who is also Wanaka's chief Civil Defence co-ordinator, said he was watching lake levels closely.
Rainfall, which was steady throughout yesterday, was not as heavy as predicted, he said.
Lake Wanaka was starting to rise late yesterday afternoon, recording 279.185m at 3pm, beneath its first flood alert level of 279.40m.
The Clutha River was draining out of Lake Wanaka at 654.204 cumecs at 2pm yesterday, above its first flood alert level of 600 cumecs, at the confluence with the Cardrona River, near Albert Town.
At Balclutha, the river was dropping slightly, recording 1209.037 cumecs at 2pm, but still above its first alert of 1150 cumecs.
Mr Purves said that as the rain fell throughout the Clutha catchment it would not be until today that its impact on the river could be assessed.
Washouts and erosion caused by heavy rain and high lake levels had closed three walking tracks, Queenstown Lakes District Council parks manager Gordon Bailey said yesterday.
He said the Glendhu Bay track beside Lake Wanaka, the Wanaka Outlet track and the Kelvin Peninsula walkway at Queenstown would be closed for at least two weeks.