Fish poo has enabled River Murray researchers to detect a critically endangered species in wetlands in South Australia without actually having to spot one.

The Murray hardyhead was once common in creeks and rivers in the Murray-Darling Basin, but its numbers have declined since European settlement.

In recent years, the fish has been detected only in the Lower Lakes or near Berri, but recent e-DNA testing reveals its presence at the Riverglades near Murray Bridge.

E-DNA refers to traces of genetic material obtained from environmental samples, rather than DNA taken directly from an organism.

Environment Minister Ian Hunter said the method "essentially works on the basis of fish poo".

Sampling e-DNA traces in water allows scientists to monitor a wetland area without using nets. ( Tom Fedorowytsch: ABC News )

"We don't need to go catch specimens anymore to ascertain that they're there. We can actually just check by taking a water sample and screening it," he said.

"[Researchers] sample the water and they break that down into DNA fragments, they then cross check those DNA fragments in the water with the library of DNA which they hold centrally."

Water sample analysis has also revealed evidence of 13 other species in wetlands near Mannum and Murray Bridge.

Project manager Dr Karl Hillyard said sampling using e-DNA allows scientists to monitor the area without using nets.

"It's great to see the species returning, proving the environmental restoration projects we're carrying out at the River Murray are having a positive impact and delivering on Basin Plan objectives," he said.

"We can also rapidly survey a range of sites looking for threatened or pest species, whether they be fish, frog or invertebrate, to help us plan more focussed investigations."

The three-month trial was undertaken by the Environment Department and the Australian Centre of Ancient DNA.