"We would like to assure all our residents and thousands of delegates attending the climate change conference that our drinking water was not affected by floods," acting head of health at the municipality Dr Ayo Olowolagba told Sapa.
Fears were raised after the city announced floods had caused sewers and certain waste water treatment plants to overflow.
Olowolagba said there was no need to panic.
Heavy downpours on Sunday night, hours before the start of the Cop17 climate change conference, damaged properties and claimed five lives.
Olowolagba said it was possible certain water bodies had been contaminated with sewage and that this may pose an increased risk to public health. Sea water at beaches near river mouths may pose a public health risk due to high bacterial loads.
"Swimming at such beaches is therefore to be discouraged," he said.
Rivers and storm water drains were also likely to be contaminated and the public was urged to avoid contact with water from them.
"People who drink water from the drivers should boil their water. We are monitoring the situation. The warning we have issued is a precautionary measure."
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