"That's not what we're dealing with here. What we're dealing with is systemic failure to properly manage and supervise multiple parts of this council's infrastructure."
An Otago Regional Council investigation began in November 2019, after complaints about the Owaka and Stirling sites.
Staff soon found the problems ran far wider.
Over a week, regional council enforcement officers visited those plants as well as Kaka Point, Lawrence and Tapanui.
Lawrence appeared to have been abandoned, court documents said, and presented as an overgrown, stinking shambles.
Officers found "a strong sulphurous and ammonia-like odour ... pungent, incredible and really overpowering".
One described it as "smelling like rotten eggs combined with decayed chicken when left in the sun".
The oxidation pond was murky with algal growth, scum and sanitary debris floating in it.
At the discharge point into Tuapeka Creek they found black sewage fungus and sanitary towel plastics, and there was no record on site of any maintenance undertaken.
It was a similar story at Tapanui, where the power had also been deliberately turned off and wastewater was totally bypassing the treatment system and flowing into the Pomahaka River.
The presence of E. coli bacteria was found to be at more than 22 times the acceptable level there, the court heard.
District council staff admitted there had been no upkeep at some sites since March 2019.
The council had contracted City Care Ltd in July that year to take care of the 11 plants in the region but it had allegedly taken a "hands-off approach".
Staff would drive past the sites rather than enter to check whether things were working, it is alleged.
City Care faces 12 charges but has pleaded not guilty.
Despite contracting City Care to do the job, the Clutha District Council had a responsibility to provide some oversight and confirm the work was being done, Judge Dwyer said.
"[It] failed miserably and totally in that regard. Put simply, it hoped City Care was doing the right thing but did not ensure that was the case."
It was, the judge said, "reckless in the extreme" and the failures could only be described as "egregious". He fined the council $488,253 plus court costs.
And it was not the first time the district council had been pulled up for unlawfully discharging contaminants.
The council was fined $21,000 in 2018 after human waste and toilet paper ended up in the Clutha River at Balclutha.
That fiasco should have put the district council on notice about the need to manage its sewerage network properly, Judge Dwyer said.
Mayor Bryan Cadogan, who attended yesterday's hearing with other councillors and officials, said he was "deeply embarrassed" by the situation and apologised to ratepayers, communities and iwi.
Defence counsel Michael Parker told the court the council had moved to immediately rectify its errors and was now working closely with the regional council.
There had been an internal review as a result of the prosecution and a disciplinary process which had "outcomes for present and past employees".
"Shake-up would be an understatement of what has occurred at the council," Parker said.