Dunedin's Water of Leith could be home to thousands of smolt by the end of the year thanks to the Dunedin Community Salmon Trust's breeding programme.
The trust began a month-long egg harvesting and fertilisation initiative yesterday.
Trust chairman Brett Bensemann said each hen (female salmon) contained about 4000 eggs and about 2000 eggs would be fertilised from each hatchery hen, compared with only 4-10 eggs from each hen in the wild.
Jacks (male salmon) and hens used at the hatchery were 3 years old and came from the Leith.
Hens had to be killed for their eggs to be harvested, but they would die as part of the natural spawning process anyway, he said.
In the past two years, 500,000 smolt had been released through the programme.
"Dunedin has a unique salmon situation mainly because all throughout the South Island they go from rivers to the ocean.
"In Dunedin they go from rivers to the harbour to the ocean, so we need to protect that.''
The salmon used in the breeding programme were returns from 138,000 smolt released three years ago, Mr Bensemann said.
He was pleased with the strong orange colour of the eggs harvested so far.
"The eggs are a really good colour, so we know we have good stock. We work with all the salmon providers in the South Island, so genetically they are very good.''
The eggs harvested yesterday would be released as smolt in December.