Blue-green algae concentrations in Lake Tuggeranong are more than 100 times the levels recommended for safe swimming and could be dangerous for asthmatics.
A recent sample of the lake at the Kambah inlet found about 5.67 million dangerous algae cells a millilitre, ACT government data shows. That is about 5.3 million more cells than in Lake Burley Griffin's 10 sample areas, combined.
A sample taken near Lake Tuggeranong's dam wall found nearly 682,000 algae cells a millilitre.
But the actual levels would be even higher than what is shown in official records, University of Canberra water ecologist Ross Thompson said.
"They're taking an integrated sample of just the water itself," Mr Thompson said.
"When we get to very high cell counts, it starts to froth and form accumulations or 'rafts' of cells on the surface. There will be almost pure foams of blue-green algae on the surface of the lake at the moment."
At its worst, blue-green algae could make neurotoxins that destroy nerve tissue and be potentially deadly to animals and humans. But at this stage of the blooms, people with respiratory conditions, such as asthma, would be most at risk out of the water.
"As those rafts wash up on the shore ... [they] dry and the cells become airborne," Mr Thompson said.
"When you get these dried cells they can basically turn into a dust that's quite aggravating to people."
Humans could have severe skin reactions if they decided to get in the water but, "Most people don't want to jump into a slimy green lake anyway", Mr Thompson said.
It was more likely dogs that would jump in the and get a rash or skin irritation.
"This is one of the worst blooms recorded at Lake Tuggeranong. It's extreme," Mr Thompson said.
Of all the algae at the lake's Kambah outlet, 100 per cent was dangerous blue-green algae. Of the algae at the dam wall, about 99 per cent was blue-green and less than one per cent was regular green algae.
Lake Tuggeranong has been closed to primary contact activities, such as swimming and bathing, since December 6 last year. It is still open to secondary contact activities, such as rowing and boating.
Blue-green algae levels in Lake Burley Griffin have fallen dramatically in recent days, from about 4.62 million cells a millilitre across the lake's 10 areas to about 361,000. Much of the lake remains closed to primary contact.
Of the territory's ponds, Gunghalin pond had the highest blue-green algae count with 11,454 cells a millilitre. Lyenham pond had the fewest amount with 1078 cells a millilitre.
Water moves more quickly through Lake Burley Griffin and gets stirred up more by the wind than in Lake Tuggeranong, Mr Thompson said. This helps disperse and get rid of blue-green algae blooms.
The lake also had higher nutrient levels than Lake Burley Griffin and the water near Tuggeranong town park had recorded bacteria as well as blue-green algae. Bacteria that officials test for, enterococci, are normally found in humans' gastrointestinal tracts.
"The nutrient loads that Lake Tuggeranong is receiving are very high," Mr Thompson said.
"Our second stage of research is finding out where those nutrients are coming from. Its something that is still to be determined."