Heavy rain is on the way for the lower South Island.
MetService says up to 300mm is expected to fall from late Tuesday afternoon and throughout Wednesday.
This will affect much of Fiordland, Central Otago and South Westland, with significant falls in the headwaters of Lakes Wakatipu and Wanaka.
These lakes are already high, due to the spring thaw.
Queenstown Lakes District Council has warned retailers in low lying areas of Queenstown and Wanaka to be on alert.
However, emergency management officer Brendan Winder does not expect Lake Wakatipu to flood.
The lake is several centimetres below the first flood warning indicator.