Lake Ngaroto near Te Awamutu has a health warning due to a cyanobacterial bloom - an anticipated event in warmer weather.
Lakes Whangape and Waikare also have cyanobacterial health warnings but Waahi, Hakanoa, and Rotoroa (Hamilton Lake), which are tested regularly, remain below the warning level for cyanobacteria.
The form of algae produces toxins harmful to humans and animals exposed to or swallowing the water where the algae grow.
Waikato Regional Council runs tests during the warmer months.
"During blooms, lakes should not be used for any activity that involves skin contact with the water. Swallowing water from lakes affected by blooms should also be avoided," medical officer of health Dr Dell Hood said.
"Scums are a particular risk because they contain a high level of toxins. If contact with scum does occur, skin should be rinsed clean and clothing changed as soon as possible. This warning is particularly important for children.
"If people still choose to use the lakes when warnings are in place, or any other lake where there are visible changes to water colour, they should shower and change their clothing as soon as possible afterward, even if no symptoms are noticeable," she said.
Symptoms include rash, skin and eye irritation, allergy symptoms such as hayfever and asthma and possibly stomach upsets including diarrhoea and vomiting.
Waikato Regional Council no longer routinely tests Lake Kainui but caution is advised for users because of its history of cyanobacterial blooms, which can spread quickly in favourable conditions.
The Waikato DHB Population Health Service would like to be informed about health problems that develop after exposure to any of the Waikato lakes. Health advice is also available from the Population Health Service on (07) 839 8899 in and out of hours.
The latest information on cyanobacterial cell counts is available from Waikato Regional and other local councils.