The salmon were raised in a nearby hatchery and spent about six months in a tank at the aquarium.
They weighed between 200g and 600g and will spend about five years out at sea before returning to the harbour to breed.
Dunedin is reportedly one of two places worldwide where salmon can be caught within 500m of a major metropolitan city - the other being Vancouver in Canada.
Volunteers of the Dunedin Community Salmon Trust and members of the Hen's Jacks and Sprats Club were also involved in this week's salmon release.
Trust chairman Brett Bensemann said Dunedin was experiencing a "salmon rush" similar to the gold rush of yesteryear.