Scientist Sue Clearwater said the species known as Kākahi were once a valuable food source for Māori.
They also play a crucial role in detecting the health of waterways, but all three species are in decline.
Dr Clearwater has been leading research into Kākahi for the last few years, and said a University of Waikato doctoral student had recently found a clue around how to help prevent it.
Michele Melchior has discovered that the species use different reproductive strategies and that one in particular, that can live for more than 50 years, is dying out faster than its counterparts
Her PhD is part of the research programme called Cultural Keystone Species funded by the Ministry of Business, Innovation and Employment.
Dr Clearwater said the discovery could potentially provide scientists with the tools to save the species.
"This particular species can live a really long time - up to 50 years or more, but if they're not reproducing enough young they're not replacing themselves so they slowly die out and become a geriatric population."
The NIWA research shows that Kākahi were thought to reproduce by releasing clouds of larvae into a waterway. The larvae attach themselves to passing fish and "hitchhike" upstream to a new habitat where they fall off, settle and grow. They transform from a larva into a juvenile mussel during this "parasitic hitchhiking" phase.
Anything obstructing the carrier fish, including pollution and sediment, spoils the chances of the population surviving, the research shows.
"If these mussels are luring in a fish that maybe can't swim very well - which is what we think is happening, then any barriers to that fish getting to the mussels may mean that's why they're dying out faster than the species that can still attract fish getting past these barriers," Dr Clearwater says.
One species of freshwater mussels is found throughout New Zealand, but the species upon which Ms Melchior has made the discovery is found mainly in the northern part of New Zealand.
She has found that this larger Echyridella aucklandica species, mostly found in the Waikato northwards release their larvae in ways similar to how fly-fishing lures attract certain fish species.
She said as far as they know, this is the first known freshwater mussel species outside of North America to use these lures that mimic fish food items, as a strategy to attract and attach to fish.
Dr Clearwater said Ms Melchior's discovery was a big leap forward.
"It provides us with another piece of the puzzle towards understanding the mussel lifecycle, and it points to what we need to do to conserve and restore the species."
Dr Clearwater admitted to developing a fondness for Kākahi, despite describing them as the "cabbage of the aquatic world" - okay to eat but probably not the most favoured of foods.
"There's something quite primal about collecting nice big mussels from a stream, just like collecting tua tua at the beach. Also the adults can be old and tough, but the juveniles are so sensitive. That's what makes them so fascinating."
Kākahi are often found tucked under banks, in shady pools and partly submerged in shady, soft-bottomed streams.
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