Council ratepayers and iwi have footed the bill to clean up New Zealand's waterways to the tune of $94 million under the Government's Freshwater Improvement Fund in 2017, dwarfing the agricultural industry's direct contribution of just over $1 million.

A total of almost $97 million was raised by applicant organisations for freshwater cleanup projects in 2017, with the Government also contributing almost $44 million to the applicants' various projects as part of the deal.

The agricultural industry's only contributions to the Fund in 2017 have been from Beef and Lamb NZ with $265,000, the Foundation for Arable Research with $555,000 and Tawapata South Inc, who own a beef and lamb operation, with $260,331.

But the National Party says farmers are making their own financial efforts to clean up fresh water bodies through other avenues, and are themselves targeted as ratepayers.

Green Party water spokesperson Eugenie Sage says the distribution of funds from ratepayers compared to the agricultural industry, which is among the largest polluters of New Zealand's fresh water, is unjust.

Nick Smith and Eugenie Sage Source: NZ Parliament

"The problem is it's the public, either taxpayers or ratepayers, and iwi who are having to be the principal funders of water cleanup," Ms Sage said.

She added the average urban ratepayer is "probably not" aware they are essentially paying the same amount to clean up New Zealand's fresh water as farmers individually, under the Freshwater Improvement Fund.

She said that in Canterbury, where more than 60 per cent of the irrigation in New Zealand happens, the freshwater work has largely been funded by Christchurch residents.

"So city people are funding the cleanup."

However, National Party environment spokesperson Nick Smith says urban ratepayers are themselves large polluters of New Zealand's freshwater, and farmers are actually paying targeted rates in many areas to help directly generate the money for these Freshwater Improvement Fund grants.

"It is estimated farmers have spent over $1 billion over the last 10 years of their own money on the management of freshwater," Mr Smith said.

"That is in terms of more efficiently using the water, things like improving the effluent management of ponds, the 30,000 km of fences that they have installed.

"The Greens constantly make the water quality issue solely an issue about farmers when the facts actually show it is a broader issue than that.”

Mr Smith said he was "absolutely" comfortable that farmers were paying the correct proportion of funds towards Freshwater Infrastructure Fund grants relative to the extent they pollute the waterways.

However, Ms Sage said the financial contribution of farmers is an obligation of doing business using water which is a community asset. And she pointed out that agriculture is not part of the Emissions Trading Scheme and doesn't pay a resource rental on water.

To apply for a grant to clean up a New Zealand waterway under the Freshwater Improvement Fund you need to be a legal entity and have raised at least $200,000 for the project yourself. The Government will then double the amount raised.