"We have recovered 12 lifeless bodies that have been transfered to our Miami Beach base," said US Coast Guard spokesman Luis Diaz.
Nineteen people, 17 passengers and two crew, were aboard the seaplane, which belonged to Chalk's Ocean Airways, a small tourism company, Coast Guard Petty Officer James Judge told CNN television.
The plane crashed in shallow shark-infested waters in the city of Miami Beach shipping lanes near the coastline.
The charter airplane took off Monday afternoon from Watson Island, located in Biscayne Bay, between Miami and Miami Beach, on a trip towards the Bahamas, and crashed soon after.
"I saw a plume of smoke," Coast Guard spokesman Dana Warr, who was near the crash site when the plane went down, told reporters.
"It was a couple of hundred feet in the air" when the craft plumetted to the ocean, he said.
Small Coast Guard crafts and helicopters sped to the crash site. Civilian craft also sailed to the area to help.
The underwater airplane was visible from the air, as Coast Guard dives plunged into the water seeking survivors.
The plane was a 17-passenger Grumman G-73T Turbine Mallard, a twin-engine amphibious aircraft capable of operating from water as well as land-based airports, according to the company website.
The airline touts itself as "flying since 1919 - serving the Bahamas and Florida."