Farmers could be charged $100 for every animal found in waterways as the Government moves to clean up the nation's water supplies.

However, the Opposition says proposed regulations do not go far enough to stop livestock polluting rivers.

The new measures were announced today by Environment Minister Nick Smith and Primary Industries Minister Nathan Guy.

Their consultation document features 23 initiatives, including the requirement to fence off dairy cows and pigs from waterways by July next year.

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All other livestock will progressively be included in the regulations by 2030, except for sheep and goats, which do less damage to waterways, the document said.

Dr Smith said the Government was also proposing a fine of $100 an animal, up to a maximum $2000, if livestock were caught in waterways. Repeat or more serious offenders could still be prosecuted in court.

Other initiatives include:

• Strengthening the national requirement on councils to set objectives and limits for fresh-water quality and quantity in a way that is consistent around the country.

• Standardised water permit conditions on efficient use of water, and minimising nutrient loss.

• Improved iwi involvement in council development of water plans and water conservation orders.

• An additional $100 million clean-up fund for lakes, rivers and wetlands.

Dr Smith said in a speech at the Bluegreens Forum in Tekapo that the regulations would improve water quality, enable better economic use of water and help iwi to have a say on water-management decisions in their rohe (tribal territory).

"If I had a dollar for every complaint over cows crapping in our favourite swimming, fishing or kayaking spot, I reckon I'd be wealthy," he said.

"It is not just this direct pollution but the problem of cows, deer and pigs trampling stream margins and adding to the sediment and nutrients entering our waterways."

However, Labour's environment spokesman, David Parker, said regulations persisted with the current inadequate minimum standard of wadability for rivers, which meant a lot would not be clean enough to swim in.

And while the introduction of a compulsory macroinvertebrate index was good, Mr Parker said, it wouldn't keep rivers clean; it would just help to measure how dirty they were.

Green Party water spokeswoman Catherine Delahunty said there needed to be a national moratorium on further dairy conversions to protect areas such as Waikato lakes and rivers and the Mackenzie Basin and reduce fresh-water pollution.

It also failed to recognise the Treaty of Waitangi and had relegated iwi and hapu rights as a "right to have a say".

"The consultation document may sound like a step forward," Ms Delahunty said, "but it is in a context of weak overall standards which do nothing to protect the birthright of our children to swim in clean water, let alone the restoration of our native fish species."

Public submissions on the proposals close on April 22.