The ACT and federal governments finally signed off on an $85million plan to tackle the territory's polluted waterways late last month – almost six years after the federal government allocated the money for territory water projects, including an abandoned plan for a desalination plant.

But ACT Southern Catchment Group, Tuggeranong Lake Carers and Tuggeranong Community Council are concerned about what funding might be allocated to the unhealthiest body of water in the territory – Lake Tuggeranong.

During a funding announcement Minister for Environment and Sustainable Development Simon Corbell verbally excluded Lake Tuggeranong from examples of government priorities – Yarralumla Creek, Fyshwick and new development areas in Lower Molonglo and West Belconnen – although it has continuously been listed as one of the six catchments included in the project.

Emeritus professor of biochemistry and water quality expert Dr Ian Falconer has dubbed Lake Tuggeranong as the worst of the territory's lakes, ahead of Lake Burley Griffin.

Few recommendations outlined in a 2011 report commissioned by the ACT Commissioner for the Environment – widely considered a blueprint for healthy waterways – have been pursued.

ACT Southern Catchment Group chairwoman and Tuggeranong Lake Carers convener Glenys Patulny was concerned about the security of funding for the lake, a portion of which was originally earmarked for two wetlands in Tuggeranong.

"My biggest concern is there is no guarantee we will get something; we've been identified, it doesn't necessarily mean we're going to get it," she said.

In a letter to Minister Corbell, Ms Patulny and Tuggeranong Community Council president Eric Traise expressed concerns about the lake and a two-year monitoring program.

Most of the funding allocations will not be realised for another two years with monitoring and analysis to take place before works begin.

However, the catchment group's waterwatch program has seen close to 50 individuals and groups monitor the lake's health for a number of years already.

Ms Patulny was worried results drawn from the two-year monitoring would not be comparable.

"I can understand they want to do testing but the thing is it's comparing apples and oranges," she said.

"We've had ongoing problems [at Lake Tuggeranong] for six years. When you build a new development there is sediment for a couple of years, then things settle down. So if they do testing [in areas of new development] next year, it's not going to necessarily reflect what it is going to be in a few years."

Ms Patulny was particularly worried about the security of the lake as, unlike Lake Burley Griffin, Lake Tuggeranong was solely an ACT government responsibility rather than a combined federal and territory government responsibility.

A spokesman for Minister for Environment and Sustainable Development Simon Corbell assured the community Lake Tuggeranong was a priority included in the funding program.

He said consistent monitoring was a Commonwealth government condition so waterways could be compared and ranked based on priorities and realisable benefits.

"Where data is already available, this process will serve to confirm trends to add credence to business case development and inform the final Commonwealth decisions as to funded projects," he said.

"An augmented data collection regime will also serve to analyse the effectiveness of existing ponds, wetlands and other water quality control measures to inform the best approaches to new infrastructure.

"Each of the sub-catchments selected were on the deliberate basis of a representative sample of different catchment types and water management issues across the ACT ... This was with a view to being able to establish potential treatment trains in each that would better inform future catchment treatment in similar catchment types both within the ACT and more widely across the Basin.