Mr Hughes said the lime would filter down through the water, settling on the sludge that is generating the stench.
"We knew lime would probably fix the odour but we were unsure what impact it would have on the ponds' overall operation," he said.
But he said BTO Cardno staff said it would have no long-term effect on the facility.
"If it doesn't work initially, then we can re-dose it in 10 days' time."
The council also gave its chief executive officer, Kevin Ross, authority to allow a direct discharge of trade waste into the sea, but that was accepted as a last resort and only when hydrogen sulphide levels in that waste were at unacceptable levels.
Alarms at Beach Rd pumping station are triggered when those thresholds are reached.
Mr Hughes told councillors that in a healthy pond the hydrogen sulphide bubbling up from the sludge would be broken down in the highly oxygenated top five metres of water in the ponds. But at the moment that top layer of oxygenated water was significantly shallower than that.
He also told the meeting that discharging waste to the sea would not affect the stench being created in the ponds "one iota".
"The sludge remains and that's where the problem is."
Questioned about draining the ponds completely, he said it was not a matter of simply pulling a plug. Draining could take off only the top 1.5m and pumping the rest out would take several months.
"Then what do we do with the sludge that's left? It's unacceptable as landfill. It would have to be dried out but it carries vast amounts of heavy metals, along with other waste," he said.
Since December, the alarms at Beach Rd had been set off 20 times.
Mr Hughes told the meeting that he could not blame the six wet industries that feed their waste into the system for creating this problem, because the plant was inadequately designed and could not handle the amount of community and trade waste going into it.
He said in terms of pre-treatment of their wastes, the industries had adopted different approaches. Affco and Tasman Tanning used chemicals to help neutralise their waste, while others disposed of waste off-site.
Mayor Annette Main said the council would continue to work with Horizons as it battled the stench.
Ms Main said both authorities were trying to avoid the WDC being hit with "a substantial fine".
She said the current methods being tried were not giving the council enough confidence that they would work to meet next month's deadline.
Ms Main said the council was wrestling with an emergency situation.
"The whole city is suffering because of this. I'm pinning my hopes on the lime working."