But forget flushing away your toothpaste here. By next winter, more than 5200 square metres of parkland in Tuggeranong will become a vast rain garden to catch and filter run-off stormwater. It's part of a joint $93.5 million push by the federal and territory governments to help clean up Canberra's waterways.

Leaving the days of concrete drains (mostly) behind, the Tuggeranong rain garden will treat 1800 litres of stormwater a second before it can flow into Lake Tuggeranong.

ACT Environment Minister Mick Gentleman said the project was one of at least six kicking off around the capital over the next two years as part of the Commonwealth's Healthy Waterways initiative.

"It's the biggest infrastructure project per square metre that we've ever done in the ACT...so it's quite an ambitious scheme," he said.

It also includes the creation of new wetlands in Holder, which will span 5600 square metres and hold approximately 2.4 million litres of water - or roughly the same amount as an Olympic swimming pool.

Mr Gentleman joined Senator for the ACT Zed Seselja on Wednesday to announce construction had begun on the Tuggeranong garden beside Upper Stranger Pond - a "significant milestone" in the national initiative.

Mr Seselja said stormwater run-off was the biggest source of water pollution in Australia's lakes and creeks, posing a risk to both public health and the environment.

"It's not just about cleaning up things like Lake Burley Griffin and Lake Tuggeranong...but the flow on effects downstream in the Murray Basin Darling are also very important so there's a national interest here," Mr Seselja said.

The Commonwealth would stump up $76 million out of the program's total cost in the ACT, he said, and there would be flow-on benefits for both the Molonglo and Murrumbidgee rivers.

With the Tuggeranong community concerned about water quality, Mr Gentleman said Lake Tuggeranong had been identified as a priority for the initiative early on.

Two new wetlands at Isabella Pond were already under construction, on track to be completed by November next year.

"Obviously Tuggeranong has had some some particular challenges and that's one of the reasons there is a reasonable focus on Tuggeranong," Mr Seselja said.

In the past, Mr Gentleman said, storm drains have been viewed purely through the lens of emergency, designed to funnel out water as quickly as possible.

"What we understand now is that that doesn't allow the water in to the aquifer to be treated naturally before it goes into the lakes," he said.

As part of the scheme, existing concrete drains in Monash will become home to gardens and treatment works.

Research projects into how to best manage other threats such as blue-green algae and carp were also in the pipeline, after almost four tonnes of carp were removed from Upper Stranger and Isabella Ponds earlier this year.

Mr Gentleman reminded Canberrans that dumping things like chemicals or lawn clippings down storm drains also threatened our waterways.

"We're saying to people: 'only rain down the drain'."

Still, early audits of new catchments in the Sullivans Creek area were promising, he said.

"We're seeing...new critters are coming in, birds are coming in, the water's much cleaner but also people are using it for recreation as well, so they're coming down to walk, we know one person was using it to fish."