The ACT government inquiry comes as Water Minister Shane Rattenbury said the territory may never be able to entirely get rid of algae outbreaks around Lake Burley Griffin and Lake Tuggeranong.

The investigation will be undertaken by ACT sustainability and environment commissioner Dr Sophie Lewis, and will hand down findings early next year.

She said while the method of the inquiry was still being determined, it would focus on how current waterways management practices had been working.

"We can't pre-empt the findings, but the idea is to look at what happened [in the past decade] and evaluate if that's the best way to manage the waterways," Dr Lewis said.

"I expect we'll be looking at previous implementation strategies and see whether they have been value for money."

Lake Burley Griffin, Lake Tuggeranong and Lake Ginninderra will be among the bodies of water focused on in the inquiry, along with creeks and rivers in the ACT that flow into the Murrumbidgee and Molongo rivers.

The inquiry will take place nearly 10 years after the previous major evaluation of Canberra waterways in 2012.

Along with the effectiveness of government strategies, the role of community groups and stakeholders will also be examined.

ACT Water Minister Shane Rattenbury said the new inquiry was expected to build upon the findings from the 2012 report.

However, he said it was unlikely the investigation would result in a silver-bullet solution for blue-green algal blooms on Canberra's lakes.

"We will always have to manage blue-green algae, we're never going to make the lakes perfect, [the algae] is a natural phenomenon," he said.

"But there is a range of things we can do to reduce the amount of nutrients going into the lake."

Submissions to the inquiry from the public are not expected to form part of the investigation, which is likely to instead draw on work from researchers and catchment groups.

Setting up a new inquiry into the health of Canberra's waterways was a key recommendation from the ACT's State of the Environment report that was handed down in 2019.

"We started to prepare [the inquiry] in the previous term and then the election and COVID diverted a lot of work, but this needed to be done," Mr Rattenbury said.

"There's no single, easy solution to fix the trends in the lakes, and there's still plenty of work to do."

The ACT government has previously spent $93.5 million as part of the Healthy Waterways program.

Of that, more than $30 million was allocated to helping clear blue-green algae from Lake Tuggeranong, which still remains a persistent problem.

The newest initiative, launched last week, involved placing floating wetlands on the lake as a way to absorb any nutrients that may later turn into algae.

Both Lake Tuggeranong and Lake Burley Griffin have been beset by blue-green algae issues, closing multiple times due to the heightened levels.

The algae in the Lake Burley Griffin was once so bad that it could be seen from space.

Dr Lewis said that multiple options in how to address algal issues on the lakes were on the table.

"We know waterways service multiple purposes and they are an area that are used by the community for recreation and they also have good biodiversity values," she said.

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