Divers will resume searching for other victims on Friday, police said.
Seven people were taken to hospital following the incident on the "Ride the Ducks" amphibious vehicle on Table Rock Lake, near Branson, Missouri, Stone County Sheriff Doug Rader told reporters.
At least 11 people were killed in the incident as divers finished their search effort on Thursday night. They will resume searching early Friday for about five people still missing, the sheriff said later in a news conference.
Emergency crews responded to the incident shortly after 7 p.m. (0000 GMT) after thunderstorms rolled through the area, the fire district said on Twitter.
"There was some heavy wind. It was having problems through the wind," Rader told reporters. "They were coming back toward land. There was actually two ducks. The first one made it out. The second one didn't."
Seven victims including two critically injured were treated at the Cox Medical Center in Branson, the hospital said on Twitter.
Video footage shot by an eyewitness who was on shore showed strong waves tossing two duck boats side to side. The video clip was posted online by KY3.
Life jackets were on board the boat, Rader said.