Officials suspect that thousands of dead birds washed up on the shores of Ontario's Georgian Bay were killed by botulism, Ontario's Ministry of Natural Resources said on Monday.

The ministry was cleaning up some 6,000 dead birds found scattered along a nearly three-kilometre stretch near Wasaga Beach over the weekend.

Experts say the birds may have been killed by a form of botulism that is found in the algae on the bottom of the bay.

The ministry said that samples were sent to a lab for testing and that it is waiting on the official diagnosis.

Local naturalist Bob Bowles says zebra mussels filter the water and build up a high concentration of the bacteria, before being eaten by the waterfowl. The bacteria then paralyze the birds.

"They can't lift their head up, their head drops into the water and they drown. Then their bodies float to the shore," Bowles explained to CTV Toronto.

"We've got these beautiful sandy beaches from Wasaga right up to Lafontaine and the winds coming from the northwest are washing them up on the shore line. That is why they find a new crop every day."

Bowles says he expects more birds to wash up dead in the coming weeks. The long-tail ducks migrate early, and other birds such as loons will likely be affected as they cross the region while flying south.

Locals said they noticed some dead fish on the beach a few weeks ago and a few dead birds earlier in September.

The Ministry of Natural Resources says it isn't unusual for large numbers of fish and other wildlife to die on the Great Lakes at certain times of the year.

According to the ministry, smaller-scale die-offs occur annually on the Lakes. The last one happened on Lake Ontario in 2007.

Public health agencies say no cases of human illness have been attributed to outbreaks of botulism in the Great Lakes.

Botulism thrives in low oxygen environments often found in zebra mussel colonies.

With files from CTV Toronto's John Musselman