Minister for Agriculture Adam Marshall says two million new fingerlings, including the Murray Cod species, are expected to be released into waterways this summer.

"Last year we embarked on the largest-ever fish breeding program in the history of NSW and now our modern-day Noah's Ark is taking shape," he said.

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"After long-awaited flows into the Murray-Darling river system and with our breeding program in full swing, we could see fish being returned to our state's waterways sooner than anticipated."

The minister said more than 100 mature Murray Cod would be returned to the rivers from where they were rescued last summer.

Breeding Murray Cod would stay at the government's flagship native fish hatchery at Narrandera "to continue replenishing numbers for years to come", he said.

The minister said "additional investment as part of our $10 million fish rescue strategy" would result in the breeding of about 2.5 million native fish species each year.

"Through this breeding program, we are ensuring we preserve the genetic diversity of our key native species and will be able to restock our rivers across the state," he said.

Key target areas for restocking are the Darling River downstream of Brewarrina, and across the southern basin including the Lachlan, Murrumbidgee, Macquarie and Murray catchments.

As part of the fish rescue strategy, more than 5000 fish from waterways across the state have been relocated to "safe locations" within both public and private hatcheries and sections of river with long-term water security.