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''We dispute the interpretation of figure 10 in the report,'' ECan's chief scientist, Dr Tim Davie, said.
''The report says that 'sites with worsening trends were ... in Canterbury', which is technically true, but the same could be said of anywhere in New Zealand.''
Dr Davie said data in a diagram for figure 10 in the report showed there were more sites improving than worsening for ammoniacal nitrogen, dissolved reactive phosphorous, E.coli and nitrate-nitrogen.
''We interpret this as showing a gradual improvement in water quality, although ... the improvement is not enough.
''It is the first sign of improvement and we're working hard with our communities to continue that improvement.''
The Environment Aotearoa report was prepared in conjunction with Stats NZ and stated Canterbury, with Waikato and Manawatu-Wanganui, had the highest leaching from livestock in 2017.
The number of dairy cattle in New Zealand increased by 70%, from 3.8million to 6.5 million, in the period 1994 to 2017.
The biggest increases have been in Canterbury, Otago and Southland.
During this time, the number of sheep decreased by 44%, from 49.5 million to 27.5 million nationally, and beef cattle by 28%, down to 3.6 million from five million.
Canterbury and Southland had the biggest increases in the number of cattle per hectare.
Dr Davie said the Environment Aotearoa data for groundwater covered the period 2005-14.
''Our data to 2017 show fewer sites with worsening trends in nitrate-nitrogen, but we still see many sites with worsening trends.
''This is expected because there is a significant time lag between reducing nitrate inputs on-farm until it is seen in the groundwater.''
Asked if ECan's nitrate pollution rules, introduced in 2012 as part of the Land and Water Regional Plan, were not tough enough, even though ECan said they were the toughest in the country, Dr Davie said it took a long time before on-farm changes were reflected in the monitoring results.
''The rules introduced in 2012 have had an impact, with dairy conversions plateauing for example. Specific rules for a number of subregions are even tighter, with more on the way.
''We are confident that these limits, together with on-farm good management practices and audited farm environment plans, will turn things around.
''It will take time, but it will happen.''
In responding to the Aotearoa Environment report, Fish & Game said regional councils around the country had failed to protect the environment for future generations and that Canterbury had more water consented for take than was available in the rivers.
''We believe Fish & Game were reacting to figure 18 in the report,'' Dr Davie said.
''If this is the case, then Fish & Game have failed to understand the fine print at the bottom of the diagram where it states 'it does not take restrictions on water takes into account.'
''There are irrigation restrictions, referred to as minimum flows, on all Canterbury rivers, which mean when the river flows are below set amounts then the irrigator cannot continue taking surface water.''
Dr Davie said 85% of the Farm Environment Plans required were in place and had been audited at least once or would be within the next year.
In its response to the Environment Aotearoa report, Federated Farmers environment and water spokesman Chris Allen said there were significant gaps in data.
''There's grim reading on many of the biodiversity, pollution, water quality and greenhouse gas indicators but they're across the board - rural and urban, industry, manufacturing and all primary sectors, right down to the individual choices people make about their transport, water use, waste disposal and so on.''
Greenpeace NZ said the report was a ''comprehensively damning'' picture of the dairy industry.
-By Chris Tobin