More than 60 big and small cod have been found dead in the water and up on banks at Yerrabi and Gungahlin ponds. Theories on why the fish are dying range from pollution from upstream construction, weed spraying, and a natural condition known as black water caused by a breakdown of leaf litter.

An ecologist who declined to be named said identifying  the cause of fish kills was difficult, and dying fish, as opposed to dead fish, would provide a clearer picture.

The ACT government will be working with experts from the University of Sydney to further sample Murray cod from the pond. Aquatic ecologists will be "electrofishing" on Tuesday to sample fish from the area.

"Electrofishing" uses electricity to stun fish and is a common scientific survey method

Cod believed to be up to six years old have been found belly-up over the past two weeks. Fishing enthusiasts fear whatever is killing the cod will continue spreading downstream into Lake Ginninderra and the Murrumbidgee River.

ACT Environment and Planning directorate cannot say whether chemicals have been used recently to treat sediment layers of water upstream of Yerrabi Pond.

"Flocculants choice is generally not specified by the Environment Protection Authority, industry is able to choose the most appropriate flocculent for a particular situation," a spokeswoman said in a written response.

According to government agencies, routine spot spraying of weeds in granite areas and garden beds in parks within the catchment has taken place but not directly near Yerrabi's foreshores.

"Minimal amounts of the herbicides Roundup and Simazine were applied to weeds, minimising the risk of chemicals polluting the waterways and harming the fish," the spokeswoman said.

Yerrabi Pond is included in monitoring for Canberra's major lakes and ponds.  Sampling occurs eight times a year for dissolved oxygen, temperature, acidity, conductivity, faecal coliforms, nutrients, algae and turbidity.