The Government is pouring millions of dollars into fencing and riparian planting along the Kaipara Estuary to protect it from pollution, including from livestock faeces.

Prime Minister Jacinda Ardern and Environment Minister David Parker made the announcement today during a visit to a Northland farm near the Kaipara Harbour.

It is New Zealand's largest estuarine ecosystem, a 640,000ha catchment with many inflowing rivers that cover the Auckland and Northland regions.

But its rare ecosystems, which are a juvenile habitat for white sharks and snapper, and a natural habitat for orca and many birds, including the critically endangered Fairy Tern, are increasingly clogged with sediment and mangroves.

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"Every New Zealander should be able to swim in their river without getting sick," Ardern said.

"Sadly, half of our monitored swimming sites are not safe for swimming."

"We need to reduce the pollution – nitrogen, sediment, E.coli (bacteria living in animal and people intestines) and other contaminants – from flowing through our cities and farms and into our waterways."

The Government wants a community-led response to clean up Kaipara Estuary. Photo / Supplied
The Government wants a community-led response to clean up Kaipara Estuary. Photo / Supplied

The work in Kaipara will be community-led and partly funded from a $12 million Government fund to improve catchments.

It will focus on riparian planting, fencing streams to prevent livestock from entering, and measuring sediment flow

Parker said that farmers will make their own decisions on where to plant and fence to help prevent build up of sediment in the harbour.

"This will take a generation to fix," he said.

"Most of the money in the end is going to be spent by farmers as they naturally renew their fences."

The work is part of the broader Government aim to clean up rivers and lakes, for which Budget 2019 set aside $229 million to improve land use and waterways.

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Parker said that the Kaipara work will include volunteers, iwi, local government, farmers and school students.

"Those lessons from 'exemplar' catchments like Kaipara will be passed on to others. Further exemplar catchments will be identified in coming months.

"It's our birthright to go down to our local river in summer for a swim and put our head under without fear of getting sick - and to be able to gather kai from our waterways."

In the following months, the Government will announce measures to implement its Essential Freshwater plan including setting national direction for councils on freshwater standards.