An invasive species of feral fish has infiltrated the Swan and Canning rivers, prompting authorities to warn about the risks they pose to the ailing system's health and native wildlife.

The Swan River Trust said it was investigating ways to control pearl cichlids after dozens of dead specimens were found during a mass fish kill in the Swan River last year.

The discovery confirmed the spread of the species into the main river system.

Previously it was believed it was limited to a series of lakes and drains upstream of the waterway.

It also came after the State Government in 2008 abandoned attempts to eradicate the species, which was first detected in the lakes at Altone Park, Beechboro, in 2006.

Amid the spread of other invasive fish species, including gambusia and koi carp, the trust said it was worried native fish and animals could be displaced or wiped out by the pests.

Pearl cichlids, which come from South America, are a particularly destructive species that compete with native fish for food and damage the health of rivers by muddying the waters.

Although typically associated with tropical fresh water, surveys by the Department of Fisheries have found pearl cichlids can survive and are even "thriving" in the Swan's brackish environment.

The trust's senior environmental officer, Jeff Cosgrove, said it appeared the fish found their way into the Swan River during periods of high water flow.

Dr Cosgrove said despite their spread, the pearl cichlids seemed to have a limited number of breeding locations in Beechboro and eradication efforts would focus on these areas.

"Our focus for a potential eradication attempt is the primary breeding population in the Altone Park lakes," he said.

"If we can knock out this population we substantially reduce the risk of this feral species becoming more widely established and having a negative impact on the local aquatic environment."