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In the past year, more than twice as many Otago farmers have been prosecuted for offences - mainly relating to dairy effluent and pugging - than the year before.
In the 12 months to July, the Otago Regional Council brought 19 prosecutions, up from seven the year before.
The number of infringement notices stayed static at 35, figures released by the council showed.
Council resource management director Selva Selvarajah said the numbers were a warning to land-users the council would not tolerate "gross activity".
Prosecutions resulting in fines of $179,850 were mostly for discharges of contaminants where they might enter water or disturb a river bed, and 15 of the 19 prosecutions were of farmers from the Clutha district.
In 2010-11, prosecutions resulting in fines of $105,650 were evenly spread across the region: two each in Dunedin, Clutha and Central Otago and one in Waitaki.
When a prosecution was taken, the courts imposed the sentence and fine.
The council, under the Resource Management Act, was given 90% of the money from the fine. In the past two years, the regional council received $678,418 in fines from the courts, some coming from cases that dated back to 2008: the courts allowed fines to be paid in instalments.
It cost the council $691,783 in total in staff time ($322,254), legal ($293,689) and external costs such as hiring specialist witnesses to take those cases to court.
The most expensive cases were those where the charges were defended, including one which cost the council $107,169 and another $51,427.
Fines were set by the court, not the council, Dr Selvarajah said.
"The fines are set as a deterrent by the courts."
It would take up to five years to see whether the council was making a loss or a gain financially through taking people to court. The council was not "revenue-collecting" through prosecuting people.
Although the figures showed most running the region's 390 dairy farms were compliant, a recent focus on pugging and sedimentation of waterways had brought prosecution numbers back up, Dr Selvarajah said.
South and West Otago areas featured mainly because of their tendency towards saturated soils and tile and mole drain systems, he said.
From 2007 to 2009, prosecution numbers hit a high of about 25 a year because of effluent spills and ponding.
There had been a significant improvement but there was still room for more, Dr Selvarajah said.
"The new plan change has foreshadowed no tolerance of sedimentation, bed disturbance or effluent getting to water."
Prosecution numbers would probably go up as the council's compliance unit furthered inspections, Dr Selvarajah said.