Cst. Peter Leon with the Ontario Provincial Police said a resident made the discovery around 3 a.m. Saturday.
Dead birds and fish have been washing up in the area for several weeks, but this was by far the greatest number to come ashore at one time.
As many as 6,000 dead waterfowl were scattered along a 3 kilometre stretch of shore near Wasaga Beach.
Leon said officials with the Ministry of Natural Resources and the federal Department of Fisheries and Oceans believe the fish died of a form of botulism. The birds died after feeding on the infected fish.
Strong winds and choppy surf as a result of Wednesday's intense storm may have caused the large number of birds to wash up at once.
“Winds have been very strong in the Georgian Bay area and as a result of the progression of those winds the birds did come ashore,” Leon said.
Area resident Dave Kergan said he was shocked when he saw the number of carcasses littering the beach.
“It's very odd,” he said. “I've never seen this many dead birds.”
A clean up across the shore line began on Monday. Crews from the Ministry of Natural Resources arrived to help out.
Fish from the area are still safe to eat if properly cooked. However, people are advised to keep their pets away from any carcasses.
Residents should consult with their local municipality before disposing of any dead wildlife that may have washed up on their property, Leon said.
A similar occurence took place close to a decade ago when 25,000 birds died from eating botulism-laced fish on Lake Erie.
With files from The Canadian Press and Kimberly Lamontagne