Granted a 25-year consent, a proposal to install a $8.6m central wastewater system serving both townships never eventuated, but the council was on notice that it had to upgrade the plants by September 2014.
By 2010, the start of mayor Peter Butler's term, the situation had still not been addressed and there was growing public disquiet about the toxic discharges into the river, along with the regional council's requirement to upgrade the plants.
Forced to confront the issue, the council began looking at options in 2012, rejecting a regional council offer to spray treated wastewater on land it had bought near the ponds at both sites as too expensive after its potential cost grew to $12m.
Alternatives were explored, including worm farms, floating wetlands, anaerobic digestion, constructed wetlands and a Chinese sequential batch reactor (an activated sludge system like that being proposed in the most recent review of the treatment plants).
Ranging in cost from $6m to $11m, the floating wetlands and worm farms were among the cheapest options and the Sequential Batch Reactor one of the more expensive, estimated to cost around $8m to build.
Reaman Industries Ltd's managing director Phil Read said he presented a Sequential Batch Reactor design to the council, an activated sludge system that he said was based on a proven process, with plants operating effectively both in New Zealand and overseas.
When the council was considering the options, however, he raised concerns that they only seemed to be seriously looking at the BioFiltro worm farm and floating wetland systems.
He asked them for more of a hearing to explain his system, which did not happen.
"All they were doing was looking at the dollar signs with no thought to the long-term effects."
He said he had misgivings about the wetland treatment from the start, and felt inadequate research and alternatives were gathered to inform decision-making.
"They were going down a road that did not have a proven track record 365 days a year - smaller ponds had been trialled but I believe even these have got problems."
In the light of the options presented to the council in the most recent review, he said he would advocate to the council that a complete overhaul was not needed, rather it could be a matter of rejuggling things within the existing infrastructure.
"I do not think they need to spend the money these consultants are talking about."
Another person to raise red flags about the existing treatment's ongoing failure to meet compliance was councillor Andrew Watts, who served one term on the council from 2013 to 2016.
Throughout his tenure he expressed frustration at the paucity of information provided to councillors about the plants' performance, and consistently raised questions over whether they were ever going to reach compliance, to which he said he never got satisfactory answers.
He said he voted against installing additional anaerobic and stormwater ponds at Waipukurau, fearing such measures were merely band-aids.
"I was the only one that voted against that as I wanted the whole thing looked at as this current council has just done."
While the capital costs of trying to remedy the plants had reached about $8m, he suspected that when other expenses related to the plants were included the total was likely to be a lot higher.
Although he had concerns from the start, these were heightened after he discovered a 2015 Massey University scoping study on the plants' operation that the councillors had not seen until he obtained it, he said.
Authored by Professor Benoit Gueiysse, it noted that in the face of ongoing non-compliance with E. coli, ammonium and dissolved reactive phosphorus discharges the plants' "treatment efficiency was overestimated and process design was based on over-simplistic design assumptions".
"In particular, no consideration was given to long-term effects, scale-up effects, and, especially, the potential impacts of hydraulic short-circuiting on treatment units receiving high pollutant loads.
"Poor design, therefore, likely explains below-expectation results at both sites," he said.
His paper also noted there had been little rigorous scientific effort made to identify the issues, causing consent breaches and testing technical solutions to solve the issues.
"The lack of understanding and reliable data will likely impair the development of efficient and permanent solutions ensuring discharge compliance. There is therefore a significant risk that future attempts to correct the process 'in haste' may result, at best, in capital loss, and at worst, in a worsening of the treatment efficiency."
With too little information to give recommendations for improving treatment efficiency, he said an independent expert assessment of the design and operation was required to identify the issues and propose remedies.
With the election of a new council, and the added pressure of trying to deal with the associated problems at Waipukurau of a powerful stench emanating from the plants, an expert assessment was completed last month, presenting the community with a hefty price tag to effectively treat the wastewater once and for all.
Mayor Alex Walker noted the floating wetland treatment had resulted in significant improvements in the quality of the discharge since 2013/14, and said the key for the council was to provide a solution that would serve Central Hawke's Bay for the next 50 years.
"This council has been clear about looking to the future - we can't be relitigating this every 10 years."
She said it was still very early in the decision making process, and the aim was to have an open conversation with the community about the options.
"We have to think about do we pipe waste and have just one system, do we have to bring Otane and Takapau into it?"
The option to irrigate to land was also still under consideration, but the mechanisms of how to fund an upgrade, of which very rough order costs had so far been suggested, were still a way off, Ms Walker said.
"We know the process will not happen in time for the Long Term Plan.
"We need people to understand that the council and chief executive are committed to proactively working through this and we are not interested in band-aid solutions."