The ACT government and National Capital Authority released about 59,000 native fingerlings, including 52,000  golden perch and 7000 Murray cod, in efforts to clean up Canberra's waters and rid them of carp.

ACT government aquatic ecologist Mark Jekabsons said the Murray cod and golden perch were the two species which seemed to do the best in Canberra's urban waterways.

"The fish are doing well. We're getting angler reports of some very good [golden perch] being caught out of Lake Ginninderra," Mr Jekabsons said.

It's hoped the golden perch will grow up big enough to eat local carp, an invasive fish. That's if they don't get eaten first.

Carp are an introduced pest and feast on juvenile native fish, carry disease and, because they are bottom feeders, constantly stir up sediment in water bodies.

This in turn muddies the water and, along with a warming climate, leads to more frequent blue-green algae outbreaks which kill off plants used by the native fish as a habitat.

But it's also hoped the baby fish will eat mosquito larvae by the banks, reducing the amount of mozzies along Canberra's waterways.

National Capital Authority lakes manager Peter Beutel said the golden perch that had been released over the years were doing fine.

"We're having a little bit of problem maintaining the Murray cod to a fishable size," Mr Buttell said.

The ACT government said it had released about 150,000 native fingerlings into Canberra's waterways in the last three financial years.

In September, local fishers said native baby fish needed to be urgently restocked into Tuggeranong ponds after they were drained without authorisation.

Upper Stranger Pond was drained without authorisation after a government contractor had left the valve unsecured.

The government had previously cleared 2.6 tonnes of dead carp after they had drained the pond, before restocking it with 2000 native fingerlings.

The Canberra Times directed questions to environment minister Mick Gentleman about whether the recent release was a response to the unauthorised draining but was provided responses by an ACT government spokesman.

"An accidental release of water from Upper Stranger Pond caused fish to be flushed into the Lower Stranger Pond, which had not been stocked. No widespread fish deaths were detected," the spokesman said.

The government released the baby fish at sites in Lake Ginninderra, Gungahlin Pond, Yerrabi Pond, Lake Tuggeranong, Upper Stranger Pond and Fadden Pond.

The golden perch and Murrary Cod released into the latter will see the strongest chances of survival after the removal of carp in 2017.