Federated Farmers says the environmental toll farming is taking on waterways is being blown out of proportion.
The regions are expected to be big winners under the new Government, but farmers have felt under fire recently, with threats of a water tax being brought into the Emissions Trading Scheme.
However under the Labour/New Zealand First coalition that tax looks unlikely.
Federated Farmers president Katie Milne says misinformation has led many Kiwis to believe a tax would save the environment.
"Irrigation and effluent and poor water quality don't go hand in hand, necessarily, at all," she told The Nation on Saturday.
While Ms Milne accepts farmers are still learning and addressing systems "from a lot of different angles", she says it's "not as big an issue as it has been made out to be".
"Those waterways in that area are actually not, as it's been reported, anywhere near the [pollution] levels that some people have said."
Election data shows rural areas in the South Island swung more towards Labour than northern, urban areas. Ms Milne says this may be because "the full story [was] not necessarily fully understood".
"Everyone was talking about the degradation and so on - people firmly believing that, basically, they're all buggered. And that's not true. We have areas where there has been decline. And in the towns as well, we do have issues, and we know that, and we're all trying to work towards making that better and doing our part where we can.
"That's just my opinion of what the swing was about, and I think that that was more of an urban-rural disconnect a little bit,,, people cling on to parts of it and the full story is not necessarily fully understood."
Freshwater ecologist Mike Joy of Massey University told Newshub before the election, the biggest impact on the waterways of New Zealand has been dairy intensification. He says it makes no sense to clean up rivers without stopping what's polluting them first.
"At the moment it's like we've got a pot of milk boiling over on the stove and what people are saying is 'let's just buy more sponges to clean it up' when the obvious thing to do is turn the stove down."
While farmers may not face a water tax, Ms Milne fears funding for irrigation schemes could be cut, potentially knocking New Zealand out as a player on the world stage.
"It's going to be really sad, actually, if they do, and I know they're talking about that pretty heavily looking at unbundling it, unwinding it. But it sets you up for infrastructure and ability to do things in the future.
"Things are going to change in agriculture going forward, and I say to people, 'I don't know what I'll be growing in five or 10 years. I may have less cows'. So the rest of the world will pick it up and will be able to be ahead of the game on us on that one."
The National Government put in about $400 million from asset sales for irrigation schemes, including $90 million in the last Budget.
Newshub.
