Chief medical officer Phil Shoemack said the warnings were not strictly enforced bans per se, but advised that people had a significantly higher risk of getting sick or picking up an infection if they swam in the water.
"It's not surprising because we have had a fairly good run of dry weather until Monday night.
"Water flows down and everything on the land is washed down with it into rivers, lakes and the harbour. That includes a lot of faecal matter from any animal - cows, dogs, cats, birds, you name it."
Dr Shoemack warned E. coli contamination could make someone quite sick. A person suffering from E. coli contamination can suffer from gastrointestinal problems such as severe stomach cramps, diarrhoea and vomiting for two to three days. People can also pick up infections.
"At this time of year, it would upset your Christmas celebrations."
Dr Shoemack said most people would not need hospital treatment but young people and frail people probably would.
The warnings came a day after a national index was released by Land, Air, Water Aotearoa offering people an online tool to let them check their local spots before they head for a dip.
The project is a partnership between 16 regional councils, the Ministry for the Environment and the Cawthron Institute.
Water quality for swimming was generally classified according to weekly sampling results and the overall bacterial risk based on longer-term sampling.
Land, Air, Water Aotearoa group chairman Stephen Woodhead said many council science teams would be working over the summer holiday period to keep people informed.
"Water quality changes so over summer council science teams monitor your favourite rivers, lakes, and beaches," he said. "A handy tip is to save LAWA on to the home screen on your mobile, for instant access to your favourite swimming sites."
