Experts say that the blame for the death of fish record temperature and low oxygen levels.
Dead fish, eels and crayfish have been found on the shoreline of Green Head, which is now covered with rotting carcasses.
Green Head resident Rod Wilson said: "This is a heartbreaking sight. I've lived here 28 years and never seen anything like it. For us it's just a local ecological disaster. "
The reports indicate that during the cleaning operation Green Head has raised more than 15,000 dead fish.
"Our biggest concern is how long will it take to everything passed," added Wilson.
Given the fact that the dead fish were in the water a week, residents are urged to stay away from the water, not to pick up bacteria.
Experts say that the water in these areas are now experiencing the highest growth in the world's temperature by 4 degrees Celsius higher than usual this summer.
Dr Brian Jones from the Department of Fisheries said: "Anyone who was in Perth last few months, with no air conditioning, they know what it means to the heat."
"With the fish as well. They are cold-blooded, and keenly feel the heat. "
This incident follows a similar case in which the United States in the waters near Los Angeles were found millions of dead anchovies.