Wanaka and Queenstown were on high alert last night, as their lake levels neared flood levels.
Some businesses began sandbagging in Wanaka last night, as water started lapping at the base of the waterside office of watercraft hire business Lakeland Wanaka.
Lake Wanaka's waters were sitting just below flood level last night according to Otago Regional Council monitors, and the MetService was predicting more heavy rain.
The Queenstown Lakes District Council is considering providing sand and sandbags in the town from this morning.
It said with the risk of flooding in low-lying parts of Ardmore St predicted by ORC modelling, it had decided to provide protection measures for concerned businesses and property owners as a precautionary measure.
The conditions and predictions would be reviewed early this morning.
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If needed, sand and sandbags would be available from the Dunmore St car park.
Roads in the Ardmore St area would also be closed if need be.
''Further periods of heavy rain are expected for the rest of this week, and additional warnings will likely be issued closer to each event,'' MetService said.
Lake Wakatipu was likely to be close to the level where water levels could inundate low lying lakeside reserves (including in the vicinity of Glenorchy) and enter the stormwater system in Queenstown this morning.
Strong winds were also forecast, which could cause waves, and boat users were urged to be aware of submerged logs and other debris.
In Wanaka, Jarvie Plumbing took the precaution about 5pm yesterday of sandbagging around the BNZ in Ardmore St, which it looks after. It would be back at 5am today to check on the building.
Other Wanaka businesses, including Lakeland Wanaka, moved equipment and fittings to higher ground.
Office manager Amanda Grant said because the building was on stilts it was all right last night, but the company would reassess the situation today.
Deep Canyon, which operates from the same building, has also moved equipment out.
General manager Ros Goulding said the company was still operational, but like many tourism operators, the situation would have an affect financially.
''It's super disruptive to everyone ... especially right on Christmas.''
Wanaka Gourmet Kitchen owner Sam Blatch said the situation was ''looking pretty serious'' about 3.45pm.
Persistent rain throughout the day, particularly heavy at times, had filled the catchments and rivers were raging, prompting the town to go on alert.
''Water is touching the little log cabin [on the lake front],'' he said.
''The main wharf is completely under water, you can't even see the posts sticking out.''
The rain also closed several South Island roads and forced the closure of the Tuapeka Mouth punt bridge on the Clutha.
A Clutha District Council spokesman said the strong river flow put the bridge in danger of being swept away.
"It's been going at 1200cumecs for the past day or so. It's predicted to get to 1400cumecs by midnight tonight."
He said it happened "every two or three years".
Trees came down around the region, and various roads were closed.
MetService forecaster Gerard Bellam said a pattern of storms reached Dunedin just before 1pm.
''They were kind of gone by 2.30. You had a period there where you had heavy rain coming out of those thunderstorms.''
This was caused by a warm northerly front flowing across the country ahead of a cold front.
Today, a nor'westerly flow would pass through Dunedin and a maximum of 23degC was expected.
There would be a short period of rain in the morning.
Authorities are monitoring two 20-foot shipping containers that are floating on the Buller River.
Buller Civil Defence said the two containers became dislodged from a property in Murchison in yesterday afternoon's heavy rain.