A freshwater ecologist believes the Government is missing the mark by getting communities to clean up waterways.

Prime Minister Jacinda Ardern on Sunday said the Government would be investing $12 million to help support farmers and communities reduce pollution from flowing through cities and farms into waterways.

But Victoria University freshwater ecologist Mike Joy says it would make more sense to crack down on intensive farming.

"The issue is, in many of these catchments, nitrate solutions from intensive farming - and fencing off rivers does not stop that problem."

Environmental Minister David Parker said that the issue of reducing pollution to waterways would take "a generation to fix", with the Government aiming to work with the community to "stop the degradation of our waterways, reverse the damage and make measurable improvements within five years".

The initiative is starting with riparian planting, fencing and restoration at Northland's Kaipara Harbour.

But Joy believes until more done is to combat intensive farming, the Government won't get the results it is after.

"My analogy is like the pot of milk on the stove boiling over and you're putting tea towels around it and here's the Government buying more tea towels instead of turning the gas off."

The Government is expected to make more announcements regarding funding to waterways in the coming months.

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