Exploring their "functional traits" - such as when or how they feed or reproduce - could prove key to restoring waterways.
"So it's not about think what organisms are out there, but rather, what are they actually doing - and what other organisms do they thrive with?" said freshwater ecologist Dr Catherine Febria, a lead researcher on the project.
The study - part of one of the Government's National Science Challenges, targeted at biological heritage - would look at what species could be having bad effects, such a tiny snail known to cover stream bottoms in agricultural waterways across Canterbury and overwhelm other species.
Trying to build a better picture of these ecosystems by gathering more data could point scientists to missing puzzle pieces, such as another species that could out-compete the damaging snail but had long since vanished.
"If we're wanting a healthy, resilient freshwater community, and we have bio monitoring data that suggests that missing species hasn't been there for decades and decades, it gives us more of a realistic expectation about how soon we think that system might recover," Febria said.
"And if we can create these designer communities and really focus on the traits that we think would overcome unhealthy resilience, then maybe that would help prescribe better restoration plans on the ground at other places."
The Government this year budgeted a further $100 million to clean up the country's waterways over the next decade, coming on top of more than $350 million spent on projects since 2000.
The 2015 Environment Aotearoa report found that while New Zealand's freshwater quality was good in areas with native vegetation and less intensive land use, there was poorer water quality and aquatic insect life - and higher levels of nutrients and E.coli - in agricultural and urban areas.
Between 1990 and 2012, the estimated amount of nitrogen that leached into soil from agriculture increased by nearly a third - something mainly put down to increases in dairy cattle numbers and nitrogen fertiliser.
About half of monitored river sites now contained enough nitrogen to trigger periphyton growth if conditions allowed, although less than one per cent of the sites had levels high enough to affect growth of multiple fish species.
Preserving our underground species
Some of New Zealand's most important undiscovered species lie beneath our very feet, living in groundwater that flows between the dark spaces in rocks and gravel hundreds of metres underground.
Some of our highly productive alluvial plains hold enormous volumes of water - most of it high in quality for us to use, with few harmful contaminants.
That's largely because of a remarkable subterranean ecosystem of microbial slime layers and small invertebrates, some up to 25mm long.
Specially adapted to living without sunlight, this ecosystem does a thorough job of filtering out and processing contaminants and many bacteria carried underground by the water.
A new study by Niwa ecologist Dr Graham Fenwick aims to identify the different populations of these important, hidden creatures.
Although they're as much a part our biodiversity as kiwi or kauri trees, and definitely play a role, scientists don't yet know what we stand to lose, and how land use might be affecting them.
Some water drawn from aquifers for town supplies contained chlorine that was routinely added to kill off any surviving bugs and, in some places here and around the world, groundwater was being used up faster than it can be replaced.
The study would use DNA profiling to identify and characterise species - many of which will be new to science - and create a new library for conservation managers, councils, iwi and other groups, Fenwick said.
"Currently, regional councils manage groundwater as a physical resource with some chemical properties - they don't consider that groundwater has any biodiversity values, nor that there are any ecosystem services that are valuable to society."
