A Florida Fish and Wildlife Conservation Commission team found the 11 dead whales Sunday.
Ten other pilot whales died last week after the pod was stranded near Everglades National Park.
The pod stranded itself Tuesday afternoon near Highland Beach on the southwest edge of Everglades National Park.
About 50 stranded whales were found Tuesday in shallow waters near the national park.
The whales were stranded in one metre of water, making it difficult for rescue teams from the National Oceanic and Atmospheric Administration, or NOAA, and Coast Guard to save them.
Six whales were dead when the rescue teams arrived and four others had to be euthanised.
The pilot whales started swimming north toward deeper waters Thursday, but a Coast Guard vessel spotted 20 whales close to shore a day later.
The whales found Sunday may have belonged to the group that swam south and ended up in shallow waters, officials said.
Researchers have not yet determined what caused the whales' deaths, but a number of factors are being examined, NOAA spokesperson Blair Mase said.
The last mass pilot whale stranding in Florida occurred in May 2011, when 16 of the marine mammals ended up stranded in Key West.
The Florida Keys were the scene of the stranding of 28 pilot whales in 2003, and many of the animals died.