Deep beneath Waitomo's rolling hills lies a maze of caves and underground rivers.

Here, NIWA researchers braved the dark waters to measure the current and hunt for fishy invaders under the twinkle of the cave's magical glowworms.

The Waitomo caves are legendary.

Famous for their enchanting glowworms and spectacular stalactite and stalagmites formations, these subterranean limestone chambers were once part of the ocean floor, but time and the elements worked together to forge these snaking passages that now penetrate New Zealand's central North Island.

The caves' existence was long known by local Māori, but they were not explored until 1887 when Māori Chief Tane Tinorau and English surveyor Fred Mace sank down into the earth with only candlelight to guide their way. They were stunned by what they saw.

Tane Tinorau wanted to share these natural wonders with the world, so opened the caves to tourists in 1889.

Today, the Waitomo Glowworm Caves are owned and protected by the Ruapuha Uekaha Hapū Trust and Department of Conservation.

Their team members include direct descendants of Chief Tane Tinorau and his wife Huti, and they host thousands of visitors per year.

But not all visitors are welcome.

Last year, NIWA Principal Scientist for Natural Hazards and Hydrodynamics Dr Graeme Smart and hydrometric technician Carl Fischer were alerted to some undesirable invaders lurking in the cave system.

"It's a delicate ecosystem for the spectacular glowworms that live in the caves, so it is guarded and managed carefully," says Dr Smart.

The invaders are Koi carp, a symbol of strength and perseverance in other cultures, but a serious concern here in New Zealand.

These fish, which look like large goldfish, are not native.

They were released into New Zealand waters around 60 years ago and now pose a serious problem.

"The reason they are prized in places like Japan is because they are especially hardy, being able to survive in extreme conditions and live long lives, but their appetite means they are destroying our indigenous species and freshwater habitats at an alarming rate.

"People were worried because they may be competing for food sources in the caves, which could severely impact the glowworms and other native animals. Waitomo caves have vast spiritual, environmental, and economic importance, so it's a problem that needs resolving, and quickly."

Fast forward four months and the (aptly named) Smart Fischer team was wading waist deep in the cave's dark waters.

"The regional council has proposed building a fish barrier downstream of the caves to stop carp migrating up into them. This would be fine if it were not for the fact that these caves can flood. When the streams reach a certain height, operators must close the caves. Anything that raises flood levels, such as a fish barrier, could be a problem. And it's why they asked for our help."

To know what the best course of action would be, the Discover Waitomo Group tasked NIWA with measuring water levels through the cave system and identifying fish species that make Waitomo caves home, particularly the invasive carp. This would help them figure out whether the weir could worsen any flooding.

For Fischer and Smart, it turned out to be a bit of an adventure.

"At first, we thought this would be straight forward - we'd nip up there, take some measurements, let the council know the water levels and flows, and then we'd be done.

"But when we looked more closely, we realised that none of our modern surveying equipment would work in a cave. It's GPS operated, so functions perfectly well outdoors, but is completely useless down there. So, we went back to the good old-fashioned way of doing things. Which meant getting our feet wet."

One of the methods they used was a level traverse which involves linking water levels measured in the cave to water levels at the cave inlet and resurgence, or exit, by a path of intermediate level stations.

As the cave flows into a natural underground pipe from the glowworm grotto to the resurgence, it was not possible to follow this route and so Fischer and Smart took the next shortest route, through the Waitomo visitor centre.

"So we had this situation where people were happily sipping their lattes, and we were nestling in saying ‘excuse me, we just need to insert this tripod beside your table, not to worry, pardon me'. We had a great time."

Smart also photographed the fish species they encountered in the caves, enlisting the help of NIWA fisheries scientists to identify them.

Now, the team are in the process of evaluating their findings and planning further studies. It's likely that the cave system could need computer modelling to get a true idea of the impacts of inserting a downstream fish barrier.

In all though, Smart thought the job was fascinating.

The work was organised through Discover Waitomo's environmental manager Shannon Corkill, in conjunction with environmental consultant Michelle Archer. Dr Smart says it helped him to really appreciate why these extraordinary caves need protecting.

"Once the work had been done, I went with one of Chief Tane Tinorau's descendants on a cave tour with a group of internation visitors. It was a real experience. First off, they lead you into a large cavern called the Cathedral and ask people to sing amongst the stalagmites and stalactites. It was really moving. You then hop on the boats, and it's pitch black. You can't see a thing. Everyone was dead silent as the guide zig-zagged the boat through the cave, and above you is the most beautiful light show, twinkling like the night sky. You completely lose yourself in there. It's nature at its finest."