More than $1.5 million is to be spent over the next five years to restore and protect water quality in more than 20 Northland lakes, including some of the region's most ecologically outstanding dune lakes.

The 24 dune lakes included in the Freshwater Improvement Fund (FIF) project include nine rated as ecologically outstanding (among a dozen for which the Northland Regional Council has recently completed specific management plans), the other 15 having special management needs.

Regional councillor Mike Finlayson said the joint funding would enable significant progress to be made in preserving what he described as unique aquatic habitats and taonga worthy of protection and special care.

"They are among the rarest and most threatened aquatic habitats in the world, and it's our duty to look after these precious gems," he said.

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Cr Finlayson, who represents the council's Te Hiku constituency, home to a number of the lakes, said they provided habitat for a wide range of plants and animals including rare freshwater fish, and the funding would enable a greater effort to be made to save them for future generations.

The lake management plans formed the basis for a successful bid for funding from the FIF (administered by the Ministry for the Environment), with matching contributions from the regional council, totalling $1.565 million over five years.

The council was engaging with eight mana whenua iwi groups to develop a joint engagement approach to do the work, which would include the incorporation of matauranga Maori (traditional knowledge) in future regional council environmental monitoring.

The project would also feed into the Enviroschools' WaiRestoration projects and Te Aho Tu Roa education programmes, which would track its progress.

Work would include controlling or eradicating aquatic weeds and pest fish, removing grass carp, reducing sedimentation and fencing.

"There's also a native plant aquaculture project, which aims to remove nitrogen, phosphorus and carbon from the water," Cr Finlayson said.

The nine ecologically outstanding lakes that are included in the FIF project include Waihopo and Ngatu (Aupouri Peninsula) and Waiporohita (Karikari Peninsula).

The other 15 include Kihona, Ngakeketo North, Ngakeketo South, Te Werahi Lagoon, Waiparera (Aupouri Peninsula), Heather, Mini/Split, Ngakapua South, Rotoroa and Waimimiha North (in the Sweetwater area).

Management plans for the first nine are available at www.nrc.govt.nz/dunelakesproject