AVA- The plane was attempting to land at a Jacksonville military base in a thunderstorm on Friday night when the incident happened.
Twenty-one people suffered minor injuries and were taken to hospital, said authorities.
The plane was arriving from the Naval Station Guantanamo Bay in Cuba with 136 passengers and seven crew members on board who had "all been accounted for", said a statement from the Naval Air Station Jacksonville.
"The plane was not submerged. Every person is alive and accounted for," said the Jacksonville Sheriff's Office on Twitter.
The tweet shows two photos of the plane resting in the water.
Attorney Cheryl Bormann, who was a passenger on the plane, told CNN that the aircraft made a "really hard landing" in Jacksonville amid thunder and lighting.
"We came down, the plane literally hit the ground and bounced, it was clear the pilot did not have total control of the plane, it bounced again," she said, adding that the experience was "terrifying".
Bormann said she hit her head on a plastic tray on the seat in front of her when the plane veered sideways and skidded off the runway. "We were in the water, we couldn't tell where we were, whether it was a river or an ocean."
The passengers then helped one another climb atop one of the wings of the plane to wait for help.
An investigation into the cause of the accident is underway, said the statement.
The National Transportation Safety Board said on Twitter that 16 investigators were arriving in Jacksonville on Saturday.
"NTSB team has expertise in aircraft operations, structures, powerplants, human performance, weather, airports and other areas," the agency said, adding that it expects to brief the media later in the day.
Boeing said they would "provide technical assistance" to the NTSB at their request.
Jacksonville's mayor Lenny Curry tweeted that President Donald Trump had called him and offered help.