MetService expects more bad weather over the weekend.
There was heavy rain and wind in parts of New Zealand on Friday morning.
MetService predicts a second front will move in from the Tasman Sea on Saturday, bringing gale force winds and heavy rain to both the North and South Islands.
Meridian Energy says the Upper Waitaki hydro storage lakes are already at 97% of their average level for this time of year.
Heavy rain may force the company to spill excess water into the Waitaki river.
Several other parts of the South Island are also at risk of flooding because of the heavy rain.
Southland Regional Council is monitoring the Makarewa River while Otago Regional Council has issued a flood warning as Lakes Wanaka and Wakatipu already have significantly high water levels.
Rivers with heavy flows in parts of Canterbury are also being closely monitored.