A plume of murky sediment could blight Perth's most popular beaches for up to six months from November when a million cubic metres of dredged material from Fremantle harbour is dumped into the sea.

A mountain of sludge and limestone will be generated during Fremantle Ports' $250 million dredging operation to deepen and expand the port.

Some of the less polluted material from the dredged areas will be dumped on the western margin of Gage Roads, about 8km from the coast. A 3m deep blanket will cover 150ha of ocean floor, smothering up to 50ha of seagrass.

It could create a sediment plume which the port concedes might affect swimmers and divers as far north as Scarborough.

In an official report on the impact of the port deepening, compiled in June, the Environmental Protection Authority conceded the project would affect beachgoers.

"Aesthetic and recreational values relating to the extent of visible plume along the coast during summer will be compromised by this project," the report states. "The EPA accepts that this will be for duration of approximately 20-26 weeks and that the coastal waters will resume normal water quality once the activities associated with this proposal cease."

Independent environmental researcher James Courtney, who has studied the project for two years, warned swimmers to avoid the area.

Sediment from the dredging deemed too toxic to be dumped in open waters because it is laced with tributyltin (TBT), polychlorinated biphenyls (PCBs), organochlorines, arsenic, lead and mercury, will be used on 37ha of seabed at Rous Head.

Environmental campaigners warned yesterday that the poisons which have been trapped in the silt over the past few decades would be released and risked contaminating neighbouring Port Beach.

Lee Bell, from the National Toxics Network, claimed a report seen by port bosses showed toxic material was already leaching from Rous Head. Dumping extra material at the site would compound the problem.

"The report noted that the levels for arsenic near Rous Head were already approaching the maximum acceptable levels," he said.

Environmental scientist Peter Dingle said TBTs and PCBs, which were toxic to marine life even in minute particles, would be released into the environment.

Fremantle Ports spokeswoman Ainslie de Vos said the project had passed the necessary environmental approvals. No sediment would be dumped in the open sea unless contamination levels fell within acceptable guidelines.

North Fremantle resident and kite-surfer Michael Ma said he was worried by the pollution.

Premier Colin Barnett was confident the project would be managed properly, his spokesman said.