The Murrumbidgee River has been closed to visitors at most swimming spots this week, after bacteria levels deemed unsafe were detected at several locations.
Too high levels of enterococci, a bacteria found in feces, has closed every spot except Point Hut Crossing, with heavy rainfall likely responsible.
Bacterial levels in some areas more than triple what the ACT government considers safe, with run off from surrounding properties thought to contribute.
A cause of gastrointestinal illness, enterococci has also seen swimming banned in Lake Tuggeranong, Lake Ginninderra and the Molonglo River this week.
While the public-health impact of high-flow events is well established, health risks associated with low-flow are still being assessed.
Research by a team of Australian National University academics found either extremes were associated with high levels of enterococci over a long period, however, their modelling was unable to predict the bacteria during low-flow periods.
The researchers found an increase in pets, swimmers and babies in nappies accessing waterways during low-flow periods could result in higher bacteria levels.
Environment Minister Rebecca Vassarotti said low flow in the Murrumbidgee added to the risk of conditions that favour poor water quality.
"If this occurs, this could cause a closure of swimming spots in the summer months for everyone's safety," she said.
Ms Vassarotti said inflows into the ACT and the opportunity to prevent low inflows was largely limited to the operation of Snowy Hydro releasing water from Tantangara Reservoir.
Primary producer's abstraction of water upstream, regulated by the NSW government, also impacted inflows, Ms Vassarotti said.
Water Minister Shane Rattenbury and ACT Senator David Pocock have both backed a review of Snowy Hydro's management of the Upper Murrumbidgee, including policy allowing 90 per cent of flows to be captured upstream.
Ms Vassarotti said the amount of water flowing into the ACT at Angle Crossing was the main factor that determined water levels in the ACT-controlled portion of the Murrumbidgee River.
"The portion of the Murrumbidgee River that runs through the ACT is primarily managed for conservation," she said.
"As well as a place for recreation for local residents and visitors with several designated swimming areas along the river."
ANU Professor Aparna Lal said high visitation to Murrumbidgee swimming spots coincided with higher enterococci levels, which raised the question over whether stirring up sediment was contributing.
She said the team was currently collaborating with the Environment Directorate to better understand the level of risk for swimmers.
"Low flow conditions and high enterococci conditions present an interesting challenge and certainly one we will explore further," Professor Lal said.
Professor Lal said future rainfall variability would impact flow and turbidity, and therefore levels of bacteria.
"It is now important to identify what the sources of bacteria are to gauge more accurately what the level of risk to public health is," she said.
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