"We have a persistent problem and have decided to continue treating all diarrhoea-related cases free of charge," Harare health director Prosper Chonzi told the state-run Herald newspaper.
Chonzi warned that the situation would get out hand if the water situation did not improve.
Some suburbs in Harare go up to six days without water at a time, residents said.
"At times we can even go for five, six days without water. Right now we do not have water and we are forced to seek water from those people with boreholes at their homes," Samuel Tapera said.
In July, at least 20 children died after an outbreak of diarrhoea hit the western town of Kadoma.