Northland's environmental watchdog council says popular Northland swimming spots have better water quality than the picture painted by central Government.

Northland Regional Council (NRC) is vowing to work to further improve water quality even as the Government is widely criticised for lowering national standards so more sites pass the test.

The NRC's recently ended summer testing, involving hundreds of tests at freshwater and coastal sites, showed all were clean enough to swim at all or most of the time.

The results were released on the eve of the Government announcing its new "swimmable" freshwater quality target last week.

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NRC chairman Bill Shepherd said 93.5 per cent of the regional sites met national "guideline values" and were suitable for swimming, and 99.8 per cent in coastal areas, according to hundreds of samples taken from 13 popular freshwater and 46 popular coastal sites.

Mr Shepherd said that on the face of it, central Government's maps showed Northland had some of the country's "least swimmable" rivers, streams and lakes.

He said it was difficult to respond to those maps without sounding defensive - however, in recent years the council and Northland communities had put a huge amount of time and effort into lifting regional water quality.

Mr Shepherd said it was ironic that the latest data came as the Environment Ministry released maps showing some sections of Northland rivers - many of them not normally swimming sites - with lower quality.

The NRC believed the methodology and historic data used to determine the Ministry's tables would disadvantage Northland, he said.

Environment Minister Nick Smith revealed on Thursday the Government's aim to have 90 per cent of New Zealand's rivers and lakes safe for swimming by 2040.

However, the Government also changed the guidelines; doubling the previous allowable level of E.coli bugs - to 540 parts per 100 millilitres of water - for a rating of "excellent".

Dr Smith said 72 per cent of the country's freshwater sites were now currently swimmable - according to standards used in Europe and the USA.

Northland freshwater campaigner Millan Ruka said the move was "smoke and mirrors".

He also said the 2040 target was "way too far out and a cop-out".

Dr Smith said it would cost local and central governments and landowners $2 billion to clean-up 10,000km of waterways over the next 23 years, backed by national rules about keeping stock and human effluent out.

Mr Ruka has been scornful of the NRC's freshwater policy in which "a new kind of animal has been developed called dairy support cattle".

That could include any dairy cow not being milked, calves, breeding stock or cross-breeds, which become exempt from sustainable freshwater quality management accords between local governments and Fonterra, for example, Mr Ruka said.

The NRC's definition of "popular swimming spots" and safe water quality did not include many sites traditionally used for swimming by Maori and rural communities, he said.