One of the most significant problems associated with hatcheries is the unknown genetic effects of interbreeding between hatchery and natural-origin fish, particularly in the natural environment.
For a particular species, we essentially have 2 groups of fish that spawn in 2 very different environments: the hatchery environment and the wild environment.
Fish spawning in a hatchery produce progeny that return to the hatchery and are then used for broodstock.
Likewise, fish spawning naturally in the wild produce offspring that return to spawn naturally.
However, hatchery spawners also produce offspring that spawn in the wild, and natural-origin fish may be used for broodstock.
In the past, levels of gene flow between the two environments were largely unknown, and the genetic impacts of hatchery fish on wild populations could not be predicted.
In short, salmon biologists and hatchery managers historically had no formal plan for managing the genetic make-up of hatchery broodstocks or the genetic make-up of natural populations in watersheds where hatchery fish return.