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A sewage discharge in 2017 and a water race overtopping last year resulted in two prosecutions by the Otago Regional Council this month.
Trustpower Ltd was fined $38,250 last week after the Beaumont Race overtopped during heavy rain last year.
The regional council and Clutha District Council have agreed to a joint urban stormwater enhancement project - funded by the Clutha council - in lieu of a penalty for a sewage discharge in Balclutha on October 10, 2017.
Judge Brian Dwyer sentenced Trustpower on a charge of discharging contaminants - soil and gravel forming a wall of the race - to land in circumstances where those contaminants may enter water.
Trustpower had issued a formal apology for the incident at its Waipori Hydro-electric Power Scheme in January 2018.
Company chief executive Vince Hawksworth said in a statement the company took its environmental responsibilities seriously and accepted the overtopping occurred when works to pipe a section of the race could not cope with the heavy rain event.
He said the company took ''full responsibility'' and had taken steps to stop overtopping happening again.
Trustpower entered a guilty plea to the charge under the Resource Management Act 1991 relating to the incident.
Clutha council would remain subject to an enforcement order made by the court, requiring it to undertake actions in relation to its wastewater network.
During a sentencing hearing at the Dunedin District Court in August last year, Judge Dwyer set the fine of $21,000 for the overflow at Hasborough Pl when 18-19cu m of wastewater, including human waste and toilet paper, were discharged via the stormwater system into the Clutha by Balclutha bridge.
He questioned the usefulness of one set of ratepayers putting money ''into the pockets'' of another and ordered the two councils to discuss how the penalty could be used for the public good, in an ''environmental project''.
Clutha Mayor Bryan Cadogan said he was disappointed the regional council chose to prosecute the Clutha council.
''We acknowledge the court's decision - while this infrastructure was fully consented and worked as expected, I for one was surprised that would lead to a prosecution - but we respect the will of the courts.''