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Those in opposition include big business, farmers, local government and even Otago's conservation board, with many indicating the economic impact of the changes would be "detrimental" to the region.
About 330 submissions have been made to proposed Plan Change 6A and council analysis show 39 indicated their general support and 71 voiced their general opposition, while others expressed views only on particular parts of the plan.
The regional council says there is "universal" support for the principal of managing good water quality and "almost universal" support for the management approach of setting permitted discharge standards.
For many the support was for the approach, but concerns about how it could be practically implemented were raised in their submissions.
The Clutha Agricultural Development Board said many of the changes would seriously affect livelihoods, developments and the "very progress of the Otago province".
"If farmers are required to de-stock or to retire a large percentage of land to increase fencing and wetland plantings, then reductions in profitability, reductions in land values and reductions in economic turnover in the province is obvious."
The Cow Farm, of Ettrick, is in one of the plan's sensitive zones which had a proposed nitrogen loading limit of 10kg per ha, and owner Grant Scott said reducing its stocking rate to meet the requirement would make the farm unviable.
"I believe no economic livestock farming operation could comply with the limit and it is unlikely that any arable operation would fare any better."
The "shortcomings" of the plan change were "significant, widespread" and would potentially undermine the rural sector and the "one size fits all" approach took no account of naturally variable environments.
"The targets appear arbitrary, onerous, inflexible and unfounded."
Otago Conservation Board chairwoman Abby Smith believed the changes were overly complex for landowners and would only lead to a deterioration in water quality.
By not using more extensive consenting requirements, the process relied on "individual landowner to maintain accurate records and undertake appropriate monitoring to ensure compliance", she said.
Queenstown Lakes District Council had similar concerns that the changes could lead to a deterioration of water quality and called for assurance that significant resources would be allocated to ensure effective regular monitoring.
University of Otago Zoology Department's submission also expressed concerns about how well the plan could be expected to work in practice.
"The expectation that farmers should regularly collect discharge samples from runoff, dams and irrigation systems on their properties seems unrealistic without frequent checks from council compliance staff and resulting enforcement action under the RMA."
It would require considerable staff time and money and could create a climate of resentment among farmers.
Fonterra was concerned that practical options for farmers to do monitoring did not exist, while Silver Fern Farms was worried the rule changes would affect its discharge consents and lead to the closure of its Finegand plant.
New Zealand Institute of Forest Otago-Southland section chairman Angus McPherson said the section had concerns that without substantial modification the plan would require the forestry industry to comply with standards that were "unrealistic and not achievable even in undeveloped, pristine catchments".
Waitaki Irrigation Company believed some of the proposed rules seemed unachievable, overly open to subjective interpretation or "simply confusing".
Company member Chris Dennison, in his own submission, said the council should recognise the Waitaki plains as a special designated area. With border dyke irrigation being dominant, it would not be possible to meet the 30kg per ha limit.
"The changes in stock carrying capacity would need to be reduced in some circumstances by almost 40% to achieve this target, which would render these uneconomic."
Substantial capital investment and significant time would be need to convert properties to spray irrigation, he said.
The technology was not configured to cope with arable properties covered by the scheme, he said.
The submissions had now been circulated to all submitters for further consideration. They had until June 18 to make a further submission before a hearing was held.
Proposed plan change 6a (rural water quality)
• Sets targets for good water quality in Otago.
• Aims to meet the requirements of the national policy statement for freshwater management.
• Removes permission for rivers to be used to dilute contaminants.
• New controls prohibiting discharges that adversely affect water quality.
• Discharges that meet specified limits will be permitted.
• Limited option for consents which do not meet the limits.
• Provisions to control bed disturbance and make it easier to construct single span bridges, regarding river and lake beds and regional significant wetlands.
• Provisions to stop the use of rivers as regular stock crossings.