A Niwa assessment presented to the Otago Regional Council’s environmental science and policy committee showed while Lake Hāwea remained in "excellent" condition, Lake Wakatipu, and Lake Wānaka had declined and no longer made the highest grade.
A council staff report said the national freshwater management targets were not suitable for the deep lakes, and further, that international examples showed large lakes were "not inherently resilient", and once degradation started, it could happen quickly and be very difficult to stop.
Crs Alexa Forbes and Alan Somerville both expressed alarm when the reports were presented at last week’s committee meeting.
Cr Somerville said yesterday to his eye, the lakes remained beautiful and clean, but the trends revealed in the reports were disturbing.
Even in the cleanest of the three lakes, Lake Hāwea, chlorophyll A levels were increasing, Cr Somerville said.
"Though I’m not a scientist, I do understand that that’s a marker for certain types of degradation.
"We know that there’s a whole lot of pollution in the Taieri, we know that many of our estuaries are in a bad way, but we thought that Lake Wakatipu and Wānaka were really good, and that’s what’s so alarming, I think.
"If even those lakes up in the mountains, which are generally not surrounded by farming and agriculture and have not got big cities on them, if even those are becoming degraded, what does that tell us about how we’re looking after the environment?"
Cr Forbes said she had lived by Lake Wakatipu for 40 years and she had seen it degrade over time.
The water was not as clear as it once had been, algae appeared from time to time, didymo had appeared, and when the lake was stirred up it took a long time to settle.
"The degradation is heartbreaking. It’s definitely emotional. And we’ve been talking about it for a very, very long time.
"And it’s very ... disheartening to see nothing happen.
"Nobody seems to care."
The lakes were the heart of a hydrological system that was in trouble as it felt the impact of climate change and a range of human activity, she said.
The Niwa assessment said the lake submerged plant indicators (LakeSPI) index for Lake Hāwea was 85%, "placing it in the category of excellent ecological condition".
Its water level fluctuations limited some shallow plant community types and offered it some protection against the development of weed beds and new incursions of weeds such as lagarosiphon.
As a result its invasive species impact index was "low" at 8%.
Meanwhile, Lake Wakatipu (LakeSPI index of 72.8%) and Lake Wānaka (74.4%) had decreased from their previous excellent ecological condition four years ago to just "high" now.
Both had moderate impacts from the invasive weed Elodea canadensis and their invasive species impact indexes were 29% and 22% respectively.
As a result of the findings it was recommended Lake Hāwea was resurveyed in five years and Lakes Wakatipu and Wānaka in three years, the report said.
Also at the committee meeting, councillors received an update on the Otago deep water lakes technical advisory group, formed in April at the request of the council’s Otago deep water lakes management working group.
The group’s purpose was to provide technical advice to the management working group, chiefly regarding potential monitoring and research programmes to allow informed management of lake health, the council staff report said.
The next step for the technical advisory group was to prioritise future work needed to better understand and manage the lakes, the committee heard.