A barge is about to begin drilling in Wellington harbour in a first-ever attempt to find fresh water below the seabed.

Photo: AFP

It was hoped the drilling would find a vast aquifer that could help the city avoid the effects on the water supply of a catastrophic earthquake.

If the plan works pipes and pumps halfway between the Miramar peninsula and Somes-Matiu Island would pull water out of the Waiwhetu aquifer to supply thousands of households in the central and eastern suburbs.

It was hoped the harbour bore would provide 30 million litres a day, supplying about 20 percent of the city's needs.

It was not yet decided whether the system would run at all times or if it would only be used in emergencies.

Wellington Water's Mark Kinvig is in charge of the project.

"We're starting with a exploratory bore to understand the make-up of the soils beneath the harbour. Then there'll be a series of trial bores to understand whether we've got the right quality of water and quantity of water at that end of the aquifer.

"And if that's all successful we'll be progressing with three production bores."

It was expected to cost $10 million just to explore offshore, and if the water proved good enough probably another $35m to get the water from under 40m of mud and 10m of gravel into reservoirs.

The other option however - a cross-harbour pipeline from the Hutt bore into Wellington city which was considered several years ago - would have cost double that.

Wellington Water currently relies on major feed pipes, including along State Highway 2, which are predicted to fail in 30 places in a 7.6 magnitude quake.

After last November's big quake, the only feeder to the central city and eastern suburbs did fail, with a crack in a pipe buried 4 metres deep near the railway station.

"Parts of Wellington are likely to be without water for up to 100 days after a major earthquake," Mr Kinvig said.

"The bigger projects that we're doing will improve the resilience of the Wellington region. So the bigger bore in the harbour is a good example ... that basically brings the 100 days down to less than 30 days."

Hydrologist Dr Mark Gyopari said he trusted his own research and Niwa's seismic work this past year to avoid what would be the biggest letdown.

"We're hoping, and all the indications are, that there is fresh water where we're drilling - but there's always the chance that we hit saline water."

He said it had been known for a long time the Waiwhetu aquifer extended right under the harbour and out to the harbour entrance, where it was capped with a 40m-thick layer of mud that keeps the seawater out.

Mr Kinvig said all the resource consents were to hand and there was little environmental impact from drilling.

Wellington Water is also drilling on land, starting in Newtown next week in one of a half dozen spots in the city and Porirua where it's identified groundwater it could tap in an emergency.