The eThekwini Municipality says a water compartment is being flushed out at a reservoir in Verulam, north of Durban.
This follows the discovery of human remains in it on Friday.
Police divers were called in when workers discovered a skeleton.
The reservoir supplies several areas of water.
Community members were shocked following the discovery.
“We were consuming the water. We didn’t know how long the body has been in there,” said a resident.
He said many residents have fallen ill over the past weeks.
The municipality said it would supply water tankers to residents.