Auckland's public health boss says heavy downpours are more likely to worsen water quality and cause sickness on nearby beaches, rather than the prospect of El Nino weather.
The Auckland Council's first State of the Environment report since 2009 points to a gradual decline in the quality of marine and freshwater.
Mayor Len Brown said he would swim in some parts of Manukau Harbour despite the study showing there were high risks of getting sick.
Auckland Regional Public Health Service clinical director Julia Peters said the big issue was wild weather.
"When the weather is warm and settled the recreational water should be fine, it's really when there's heavy rain and then stormwater gets washed into recreational water that you get problems."
Dr Peters said people should not swim for about 48 hours after heavy rain.