Freshwater insects, worms and snails - important food sources for many native fish and bird species - are under pressure, but scientists are divided over what this means for the overall state of our rivers.
Macroinverterbrates have been included for the first time in the annual river quality report by Land Air Water Aotearoa, a collaboration between councils, the Ministry for the Environment and the Cawthron Institute.
Ten years of data shows populations of freshwater insects, worms and snails were "likely or very likely degrading" at two out of five sites being monitored.
Lead researcher Tim Davie, chief scientist at Environment Canterbury, admitted it was "disappointing", but he did not think the overall picture was bleak.
"They respond to different things like climate, the amount of sediment and a lot of different things," Dr Davie said.
"So they're a better overall indicator [of the state of the ecosystem] but they do take longer to respond.
"We know that our river systems can take a long time for the macroinvertebrates to improve when you start doing things to improve them."
It was positive to see improving trends for the eight other water quality indicators, including clarity, turbidity, E. coli, nitrogen and phosphorus, Dr Davie said.
However, Victoria University water scientist Mike Joy said snapshot samples of chemicals from sites selected by councils were giving skewed results.
"You can have what look like improvements because the amount of nitrate is going down in the water," Dr Joy said.
"But what you haven't accounted for is the amount of algae going up in the water.
"And that's why the invertebrates are showing virtually the opposite [to the other results] because they have been wiped out - they can't survive because of oxygen depletion and their habitat being smothered by algae. That's the invertebrates showing the true story that the nitrates aren't showing."
Many areas were showing results which were "indeterminate" - neither worsening or improving - and that was because it was hard to spot trends over a ten year period, Dr Joy said.
But for many of these sites there was 25 years worth of data available.
"And when you look at 25 years, then nearly all of them are declining."
Meanwhile, farming and irrigation and population pressure continued to degrade waterways, he said.
"I'd love to know how anyone would expect it could be getting better when we haven't done anything to make it better."
Dr Davie said there was a lot of work going on trying to keep stock out of rivers and planting alongside rivers - but the flow-on effects for macroinvertebrates took longer.
He disputed Dr Joy's criticism of councils' being allowed to select their own testing sites.
"It's not a perfect system but the site selection process is robust and there's a lot of hard work by freshwater ecologists behind it.
"If anything, councils sites are more representative of the worst than the best water quality because they know which areas need improvement."
While there was 25 years worth of data available for some sites, the report was looking at the situation nationally, which is why it only covered a 10-year period.
"Furthermore, it's really only in the last 10 years that we've been doing much of this work to improve water quality, so that gives you a clearer picture of the trends."
Jenny Webster-Brown from the Waterways Centre for Freshwater Management said almost all water monitoring showed that around a third of rivers, streams, lakes and groundwater had reduced quality due to human activities.
Previous national reports had looked at things that could affect the ecosystems - but this new data gave the first robust statistical analysis of what was happening with the ecosystems themselves, she said.
"It's a canary in the coal mine situation. It's a clear indication that things are not right and if that part of the ecosystem is suffering, then other parts of the ecosystem will be suffering."
However, professor Webster-Brown said New Zealanders could take "some encouragement that some of the things we do work".
"But [it should] also galvanise us into action on some of those other things that aren't giving us the same positive message."
Recreation fishers in many parts of the country have witnessed first-hand the decline in river ecosystems.
Ashburton man Matthew Hall, who has been fishing Canterbury's Rangitata River for 60 years, said it was "a different world" to when he was a boy.
"Thousands of salmon would come up the river from the sea each year to go to the spawning ground to spawn and sometimes there would be 50, 60, 100 caught a day," said the long-time member of the Fish and Game Council.
"Now you would be lucky if one or two were caught a day and sometimes you many days without one caught. The fishery is virtually gone."
The reasons for the decline were complex - irrigation, intensification of farming, and smaller snowfalls had sapped river levels, he said.
"It's not only fish. I've always watched the black billed gulls and the terns that nest there, and compared to when I was a child, their numbers are only a squeak to what they used to be," Mr Hall said.
"And it's all to do with the productivity of the rivers, they're just getting smaller and smaller."