Queenstown and Wānaka residents woke up to widespread flooding this morning, and are preparing for the lakes to rise even further.
MetService meteorologist Tahlia Crabtree said the region had been experiencing unprecedented rainfall.
"Generally for the month of December, Queenstown would only see approximately 60mls of rain. But they've had that much rain in the past week."
Crabtree said headwaters are causing the lakes to rise, and residents should continue to monitor the MetService website, where the warnings are constantly being updated.
A heavy rain warning remains in place until the weekend.
Queenstown Harbourmaster Marty Black said the next 48 hours were crucial and they would continue to monitor the rising levels.
Black was instructing owners of kayaks and small craft on the Wānaka and Wakatipu lakes to retrieve them, whether or not they were tethered.
Several roads are closed, and there is a high-level alert and first flood warning for Clutha at the below Cardrona River confluence.
The Queenstown Lakes District Council delivered sandbags and sand to the Wānaka CBD yesterday as a precautionary measure, and will make the decision today about whether to deliver sandbags for the Queenstown CBD, Glenorchy and Kingston areas.
The flooding is a result of heavy rainfall over the past few days.
On Tuesday, Buller Civil Defence reported two shipping containers were floating down the Buller River. One 20-foot shipping container still hasn't been located but a spokesperson said it was not a safety concern.