"It is, perhaps, the longest dry period I have witnessed in 30 years," he said.
The fish, released into the Waitaki River, were rescued during several operations as the Hakataramea River ran at low levels from the beginning of the year.
Rain late in April and during May, along with early winter snow, had helped ease the situation, Mr Hughes said.
The river was flowing at 1.27cumecs on Friday - at times this year it has been well below 1cumec.
The Hakataramea is a main spawning river for the Waitaki's trout and salmon population and important to its health, he said.
Most of the fish were rescued earlier in the year, but about 2000 were transferred in March and April.
Mr Hughes also said that a large number of fish were probably lost to birds, including juveniles, galaxids and bullies.
"Drying, shallow pools are meticulously picked clean by flocks of the most efficient fishers - a disaster for one species is a time of plenty for others," he said.
Mr Hughes said the Waitaki River had three tributaries that were considered major spawning grounds for brown and rainbow trout - the Hakataramea, Maerewhenua and Awakino Rivers.
While brown trout also spawned in the Waitaki, those three tributaries appeared to be the only spawning areas for rainbow trout and were vital to maintaining the species.
