Residents of Otematata, Duntroon, Tokarahi and Awamoko have been told to boil their drinking water.
Otematata residents are also being asked to conserve water.
Waitaki District Council spokesperson Joshua Rendell said flooding had swept dirt and debris into the catchments, which meant the water could not be properly treated and must be boiled to make it safe.
"It's looking as though the rains that are coming up are going to keep the waters quite turbid around there, so [the boil water notice will] be staying in place until early next week."
More heavy rain is forecast for this week, so it could take a couple of weeks for things to return to normal, he said.
People should also use water that has been boiled for preparing food and brushing teeth.