After being raised in the race, the fish will be released into the river in June or July next year.
Yesterday the Waitaki Riparian Enhancement Trust held an open day at its new Bell's Pond race to see the release of the fingerlings, about 5cm in length, and launch an enhancement project to improve the salmon fishery in the river.
The group has spent about 2000 voluntary hours restoring and repairing the race at Bell's Pond, on the north side of the river at Ikawai.
Earlier this year salmon were trapped in the Hakataramea River then taken to Welcome Stream, where they were stripped at the site of a new hatchery. The fertilised eggs were taken to McKinnon's Hatchery, on the Rangitata River, where they were hatched before being returned to the Waitaki Valley yesterday.
About 100 people were at the open day when the tanker bearing the fingerlings, brought down by Central South Island Fish and Game Council, released the fish.
The fingerlings will be fed by automatic feeders until ready for release.
The first adult salmon are expected to show up in the river in 2014.
Trust chairman Brent Packman said yesterday's official opening was "a very special day".
The construction of a hatchery on Welcome Stream, on the south side of the river just above State Highway 1, and restoring the race at Bell's Pond was the first stage of the trust's plans for the lower Waitaki River.
The second was to look after the fish and stage three was to build a kitset garage as a hatchery at Welcome Stream.
The fourth stage was to trap, strip and hatch fish next season and stage five was to restore riparian habitat in the lower river.
The society, which has about 200 members, was formed in April last year after a public meeting to discuss how to improve salmon numbers, which had fallen in recent years.
That led to the formation of the trust, the identification of a raceway at Bell's Pond suitable for rearing salmon and establishing a hatchery on Welcome Stream.
