Low rainfall coupled with irrigation have meant thousands of yearling trout have died in what have been reduced to evaporating puddles.
Fish and Game is urging the public to report such instances to the organisation and to refrain from liberating the fish.
It was illegal for the public to transfer fish without a permit, as illegal liberations could put a sensitive fishery at risk, and could also transfer aquatic pests such as didymo and harmful bacteria, Fish and Game Otago operations manager Ian Hadland said.
It was also illegal to use a net to take stranded fish, but "people's emotions take them over".
"We have a photo of between 30 or 40 fish in a puddle and it is easy for someone to scoop them out and think they are doing the right thing by transferring them, but they aren't," Mr Hadland said.
People were advised to let nature take its course in regards to stranded fish, and "if the heat doesn't do that for them, you never know, the next flush might take them all the way to the river".
Strandings were common in places such as Central Otago during the summer period, and Fish and Game "no longer undertake massive salvage operations".
"It's stressful on the fish, can lead to high mortalities, and transfers can put pressure on other waterways which may already be struggling."
