Lake Burley Griffin's central basin has been closed to swimmers and the Captain Cook Memorial Jet has been switched off due to extreme levels of blue-green algae.
The National Capital Authority has issued an update via the Swim Guide app on Tuesday, saying swimming would not be permitted unless it was part of an approved event, like a triathlon.
As well, the jet will be switched off until further notice.
"Swimming, diving, bathing, novice secondary contact recreation and windsurfing are currently not permitted," the update said.
"There is an increased risk of adverse health events from water exposure. Symptoms of exposure may include skin/ mucosa irritation, flu-like symptoms and gastrointestinal illness."
Sailing, canoeing and rowing is still permitted but the NCA has warned that people should be careful to limit any water exposure and should shower after contact with the water.
It came after swimming in Lake Tuggeranong was banned last month due to blue-green algae levels. The Swim Guide app says swimming is still not permitted in the south side lake.
It is recommended that people should avoid waterways for a few days after heavy rain as muck can wash up in rivers and creeks.