Cooks River Valley Association president Peter Munro said the poisoning deaths might be linked to a fish kill in December caused by aluminium from paint discharged into a stormwater drain.

"Maggots [on dead birds], which are immune to the bacteria, get eaten by fish and birds, causing it to spread up the food chain,'' he said.

A third pelican found floating on the river by Earlwood couple Juliet Barr and Peter Crutchfield is expected to die.

Australian Seabird Rescue president Marny Bonner said the botulism toxin is produced by bacteria in decaying animal and vegetable matter.

Once ingested by birds it paralyses the neck and limbs and most die within 48 hours.

"The bacteria flourishes in warmer conditions and is getting worse because of the run-off of fertilisers and dog excrement which raises the pH level in waterways,'' she said. ``It is the most significant disease, killing millions of waterbirds including waders, ducks and spoonbills

every year.''

The service rescued about 60 affected pelicans in NSW this summer.

The disease is only transmitted through ingestion and there is no risk to humans handling sick or dead birds.

A NSW Department of Environment spokeswoman said no tests were being done to confirm the presence of botulism and the department had received no reports of the two poisoned pelicans.

Botany Bay Planning and Protection Council president Bernie Clarke said people should not swim or fish in the Cooks River.

Insufficient tests were done on cryptosporidium parasites also caused by decaying carcasses and run-off, Mr Clarke said.

Report sick and injured birds to the department's 24-hour pollution line, 131 555.