Sewage flows from Masterton will be diverted into the new ponds once the pond lining and associated works are complete.
The new ponds are expected to take about one month to fill.
Pond 1A, the first of the two inlet ponds, will not be able to be completed until sewage inflows have been diverted into the new ponds, as the pipeline leading to the existing ponds runs underneath it.
Council special projects manager Ian Steer said the project is on track with the revised schedule, which would see the first pond being filled at the end of April, and they are also working within the $30 million project budget.
Hopper Construction's project engineer Luke Kirkpatrick said the inlet compound - which separates solid matter from water and pumps the inflows into the new ponds - has also been completed.
Mr Kirkpatrick said the old ponds will de-watered to 35 per cent dry solids, and the residual sludge buried in a purpose-built landfill cell on site.
Local iwi and the council have also been discussing the management of the eel population in the existing ponds.
"We've been working with Kahungunu and Rangitane and as a group we've come up with some proposals to try to encourage the resident eel population to move from the old ponds to the new ones," said Mr Steer.
The management plan and timing for this aspect of the project is yet to be finalised, but all parties would like to see the resident eel population retained at Homebush and transferred to the new ponds at an appropriate stage of the works.