"I think probably the controlling of phosphorous is probably a more important priority than controlling of nitrogen per se," said Mr McGiven.
He wants farmers' nitrogen levels to be measured and used as a reference point, and farms going over recommended amounts change their practices to reduce nitrogen.
"Every farm would have to come up with a nitrogen reference point which will cost every farmer. I don't think they've even worked out what the cost would be - probably a few thousand dollars," McGiven said.
Federated Farmers believes that the proposed riparian fencing requirements are inequitable and won't change the water quality issues.
"If that comes into play as is at the moment, the average sheep and beef farmer, the fencing requirements could be costing them anywhere between $100,000 to $700,000."
Chris Lewis, outgoing president of Waikato Federated Farmers, told the Te Awamutu Courier that the regional council's proposed new rules in the submission were not effective in helping the environment, and the costs would be too much.
"It's likely that farmers will face substantial compliance costs when the provisions come into effect. It will stifle improvements and investment, and ultimately mean an under-performing rural economy, fewer jobs and lower spending power."
The proposal also limits what farmers can use land for.
Federated Farmers believe that farmers are able to determine what the best use for land is at that time, to increase productivity.
"In effect you've locked in your horticulture use for the next 80 years so if we have a weather event and it washes all the potatoes, your price of potatoes goes through the roof," said McGiven.
Federated Farmers believed the government's Clean Water Package 2017 should be used as a provisional measure, with more proposals developed later as appropriate.
There will be further submissions in August/September, and the environmental commissioner process starts next year.
"It's potentially a big change to a farming system that we don't think really broken at the moment. We need to work through it with council, iwi and other stakeholders," said Mr McGiven.
Waikato Regional Council chairman Alan Livingston said that he felt the Federated Farmers response was very comprehensive.
Livingston was not surprised by the three main issues that were raised, as they had been debated when they drew up the plan.
"It's fair to say those are issues that are common on most submissions that were received, and of course they were the main issues that the collaborative stake holder group debated when they drew up the plan," said Livingston.
He said the council would work with Federated Farmers and other interested groups in an effort to reach an agreed outcome before the final submission is sent to the independent commissioners hearing.
"The Federated Farmers submission is very balanced in that it is looking at the environmental, economic and social impacts at the same time."