Whitebait are swimming below a park in Wellington, scientists have discovered in a project by the city’s regional council.

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Today, more than 95 per cent of Wellington’s streams flow beneath the city through pipes as part of its stormwater system, Greater Wellington Regional Council freshwater scientist Evan Harrison said.

"We're literally walking on top of fish around the city so you think when you're walking around Lambton Quay, up The Terrace.. there's actually pipes under there with fish moving through them."

Mr Harrison is part of a team at the council studying what is living in the piped streams in Miramar, Island Bay and Hataitai.

A banded Kokopu that fell victim to a hungry eel and a young whitebait that were found in the stormwater system. Source: 1 NEWS

"From the research we’ve done we haven’t found any other studies in New Zealand which are working in pipes and then connecting it to surface streams as well to know what’s moving through there.

"There’s probably minimal research around the world, they’ve focused on much shorter sections of pipes as well," he said.

A catchment in Maupuia Reserve flows into a piped stream beneath Miramar Park and connects to an outlet 1.8km away at Evans Bay.

"It must be quite a tough journey getting through there and we've always wondered how are they getting up into those surface stream areas, like half the time it could be just sheer luck that they’re finding their way up there."

It’s also a challenge for the team inspecting the drains, who had to undergo confined spaces training and walk with their backs bent over in some areas.

Greater Wellington Regional Council contractors enter a piped stream at Miramar Park. Source: 1 NEWS

"We put up with an hour and a half of discomfort to find some cool fish and document some things no one’s done before so it’s definitely worth a little bit of pain," ecology scientist Alex James said.

Over the 200 metres studied, a banded kokopu (whitebait), young whitebait and around 15 eels were found, as well as around 20 insects and invertebrates including snails and flies.

"Blew my mind really, I knew we'd capture eels down there... but actually coming across an adult banded kokopu, albeit a dead one was exciting," Alex James said about the fish that’s mid-section was missing with a hungry eel believed to be the predator.

"We've just proven now... actually seen it in the flesh that whitebait are moving through these systems."

The whitebait adds to evidence that the freshwater pipes have an ecological value.

"They're generally managed as part of the stormwater system rather than actually being a stream and there might be some mindsets we need to change there on how you manage these kind of systems as well," he said.

Mr James now wants to know if the young whitebait he found had grown up in the pipe or travelled from the upper catchment in Maupuia.

He also questions how many whitebait travel through the pipe as part of their migration every year.

The second aim of the study is to find out how the pipes can be altered to increase the rate of native species swimming through.

Suggestions the scientists are likely to discuss with Wellington City Council include roughing up the surface of pipes for whitebait to "cling" onto as they travel up the stream, adding natural objects to the pipes to improve the environment, building spaces for fish to take a break in during their journey and deepening sections of the pipe to improve water levels for large eels.

"What strikes me down there in total darkness is that the eels are still trying to hide underneath things... find a bit of broken old pipe, that’s just got a little hole under it or tree roots down there, almost every one you pick up there’s an eel or two or three underneath it,"Mr James said.

"You get some of the newer style pipes, like very smooth concrete and not rough at all, so the water would just rush through there and be quite hard for some of the fish to get up through the pipes, it’s just the velocity of it is so quick," Evan Harrison said.

Mr Harrison said the discovery of more native species in the pipe system shows why people should never empty liquids that could poison fish down stormwater drains and should wash their cars on the grass not by the gutter.