It was too early to say what would be in the final plans, as the council intended to spend three years consulting farmers, iwi and other parties before the policy was completed.
The plan would then be put out for formal consultation and was expected to be the subject of appeals to the Environment Court.
Waikato Federated Farmers and some councillors questioned what the changes could mean for the 1500 farms in the Waipa and Waikato river catchments, and suggested the plan could include contentious ideas such as capping stock numbers.
Waikato Federated Farmers president James Houghton felt it was another case of local and central government trying to tell farmers what they could and couldn't do. "What we would like to see is less rules and more results focus," he said.
Mr Houghton, whose farm crosses the upper Waipa and Waikato catchments, said he had four cows per hectare but managed his cows in such a way that his stock produced less nitrogen than an average farmer's.
Dairy NZ chief executive Tim Mackle said the policy had significant implications and care needed to be taken to get the policy right.
"That means addressing and fixing real sustainability issues while growing the economic contributions of important livestock industries like dairy."
Councillors were told the Waikato River Authority and iwi were committed to working closely with the council to ensure their policies were in line after some councillors asked if they would be duplicating rules the authority could set in 2016.
The only councillor to vote against the process, Theresa Stark, wanted the regional plan to be reviewed in its entirety rather than singling out water.
"A lot of it is the fear of the unknown but when it comes to people's livelihoods, I think that fear and concern is justifiable."
Councillor Lois Livingston said farmers should start looking at how they could improve their practices.
"Yes, there's going to be change, they are going to have to fence and plant and do all those things ... there's no choice."
REVIEW
* Regional plan change for Waikato and Waipa river catchment:
* $6.3 million over 3.5 years.
* Pre-consultation and planning until end of 2015.
* Focus will be on improving Waipa and Waikato River quality.
* The council is required to address water quality under legislation.