Federated Farmers is warning setting bottom lines for water quality is going to be expensive.
The organisation was responding to the Government's national policy for freshwater management released last week, which proposes a framework for regional councils to set minimum standards for rivers and lakes.
Water and environment spokesperson Ian Mackenzie says having cleaner waterways will come at a cost for businesses and ratepayers in towns as well as in rural areas.
Mr Mackenzie says communities need to agree on how clean they want their rivers and understand the huge costs involved.
"I mean just getting it to a bottom line ... standard between bands C and D might cost, for sake of argument, somebody said $650 million or something. To actually get the river to the state where you can swim and fish, it might cost one and a half billion dollars."
Environmental Defence Society chairman Gary Taylor says behavioural changes will be needed to meet the standards which will affect the way land is used.
"I'm sure that in some areas land use practices will have to change. When you set limits on freshwater non-point source discharges, there's only a certain amount that you can do without impacting on the intensity of the land use or even the kind of land use.
Mr Taylor says there needs to be a reasonable time frame for any changes to come into force.