Sandbags and black plastic sheets were covering the fronts of most businesses along Ardmore Street this morning as residents prepared for potential flooding.
Queenstown Lakes District Council also shut down the sewerage system along Ardmore Street and cleared stormwater drains to prevent waste entering the flood water.
It came after part of the street was closed yesterday and speed limits in the entire CBD were reduced to 30km/h.
Lake Wanaka levels remained about 25cm below the flood alert threshold.
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MetService was predicting the town would receive about 33mm of rain today, with most falling between 8am until 2pm.
A heavy rain warning was in place for Otago headwaters with up to 200mm expected between 8am Thursday and 9am Saturday.
RNZ Otago/Southland reporter Tess Brunton was in Wanaka overnight and told Morning Report water levels had remained fairly steady overnight and the main street was not yet flooded - but it was already ankle-deep along the lakefront.
"Council staff have described it as 'flooding by teacup', so the levels rise really slowly and steadily but they continue to rise. At the moment people are being urged to stay clear of the Clutha River which is ... the river that comes out of Lake Wanaka, because water is expected to surge downstream."
Lake levels were expected to continue to rise and to reach Ardmore Street, she said, with water still flowing down from the headwaters.
She said there was plenty more rain to come, with MetService expecting about 600mm - about a month's worth of rain - could fall in the space of a week.
"There's also a strong wind warning in place for Otago and that could reach severe gale between 11am and 8pm and that's a bit of concern that was raised by contractors I spoke to last night who say the wind can create a lot of really damaging wave action with debris being hurled toward buildings - but at the moment it's pretty calm out there.
"For now, it's a waiting game for both council staff and residents."
Resident Nicola Campbell recalled the 1999 flood when the water was so high jet boats were going up and down Ardmore Street. "Hopefully we don't get to that point."
She said the town and council were doing everything they could to protect buildings.
The South Island's West Coast is also set for heavy rain forecast to fall there on already water-logged hills.
The main road between Fox Glacier and Haast remains closed due to a large slip that came down yesterday.
MetService said it was unlikely there would be any relief from the heavy rain on the West Coast until tomorrow morning.