The region's waterways are coming under increased pressure due to consistently dry conditions.
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Southern ACT has come under particular stress, with the Murrumbidgee River almost ceasing to flow in December near Tharwa.
The Catchment Health Indicator Program report, prepared by citizen science group Waterwatch, monitors the region's waterways quality covering the Murrumbidgee catchment upstream of Burrinjuck Dam.
The 2019 report is based on 2040 water quality surveys across almost 100 sections of rivers and streams - known as reaches.
Of the 98 reaches in the report, only three were rated in excellent condition - one in Cooma catchment and two in southern ACT.
This was two fewer than in the previous year's report.
Overall, 59 per cent of reaches fell into the fair/poor category - a rise from 55 per cent in 2018 and 47 per cent the year before.
The report attributes the continued downward trend in 2019 to the upper Murrumbidgee catchment receiving 40 per cent below annual average rainfall.
But some of the sub-catchments fared better with the Molonglo receiving an increase in good scores.
The reports says it could be due to the reduction in rainfall meaning less sediment and nutrients are being washed into the system.
Southern ACT on the other hand showed a strong downward trend, with most of the Murrumbidgee River reaches receiving lower scores.
The report said the river showed signs of stress after such an extended dry period, with flows in Tharwa almost coming to a halt by December.
"Continued and future pressures on the Murrumbidgee River such as feral horses, climate change and Snowy 2.0 will all have impacts on water quality and quantity and Waterwatch will monitor these issues closely," the report read.
"The pressures on the catchment ramped up in the second half of 2019. Only a third of the average rainfall was recorded in winter and just half in spring.
"By December 2019 a mere 1.2mm of rainfall was recorded. This, combined with the extreme heat, saw trees such as eucalypts become stressed and go brown.
"It was at this vulnerable time that the bushfires started in the upper Murrumbidgee catchment."
Platypus numbers were mixed, with Murrimbidgee River sites appearing to support higher numbers.
There were three spotted at Point Hut Crossing and at least five at Scottsdale.
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However, Cooma and Jerrabomberra Creeks detected low numbers with just one and two individuals respectively.
Environment Minister Mick Gentleman said the new report underscored how hotter and drier seasons due to climate change are negatively impacting the region's waterways
"The ... report provides us with an early warning system for ecosystem health issues through its surveys of water quality, waterbugs and the condition of riverbank vegetation," he said.