Federated Farmers has said the regulations are "unnecessarily stringent" and would come at great cost to farmers and rural communities.
Ardern said new rules would not force farms to close.
"What's being announced today is actually a recognition that actually there is some fantastic practice being modelled by farmers in New Zealand. What we need to do is lift everyone to those standards."
READ MORE:
• Farmers face $1b bill to meet new freshwater requirements
The plan costs the changes for a hypothetical sheep and beef farm on a rolling hill at $148,500 over 10 years, and $93,500 for a lowland dairy farm.
Ardern said it was "absolutely not" a war on farming.
The Government recognised the country's economy was "hugely reliant" on rural exports, she said.
"This plan stops the degradation we're seeing and looks to the course of a generation to make sure they are swimmable again."
It also included rules which would impact urban areas and was "not about blame", she said.
The comments of Federated Farmers were in "direct contrast" to conversations she had with other members the country's rural community, she said.
"I don't think that everyone is of the same view as Federated Farmers."