The vessel was carrying 31 people when it capsized on Thursday in Table Rock Lake, near the town of Branson, leaving another seven people hospitalised and six others missing, Stone County Sheriff Doug Rader told reporters late on Thursday.
Two bodies were located by a search team on Friday morning. Four people remain missing.
Emergency crews responded to the incident shortly after 7pm (00:00 GMT), with divers deployed to assist in the search for those still missing, Rader said.
The incident occurred around the time local weather warnings were issued due to powerful thunderstorms rolling through the area.
Video footage captured from the lake's shore showed two amphibious vessels, known as duck boats for their ability to operate on land and water, struggling to move through waves.
One of the boats made it safely to shore, according to Rader.
Rick Kettels, owner of a local business on the shores of the lake, told AFP news agency the storm appeared out of nowhere.
"It just came up real quick," he said.
"I've been here most of my life and I never saw a storm this bad."
Local authorities opened Branson City Hall on Thursday evening to victims of the incident and relatives of those affected.
"This is a very trying time for all those who are involved," the City of Branson said in a statement.
"The City of Branson may be small in size but it is big at its heart."
The National Transportation Safety Board was to send a team early Friday to investigate the incident, the agency said.
Branson, Missouri, is a vacation destination popular for its theatres and country music.
The company Ripley Entertainment owns the capsized boat.
A spokeswoman for the company said in a statement that the company would "do all we can to assist the families who were involved and the authorities as they continue with the search and rescue".