The plane was carrying 136 passengers and seven crew members.
There was no water inside the cabin of the plane when rescue personnel arrived, but passengers had come out onto the wing and were then escorted through the shallow water to land.
The flight is what is called "the rotator" flight that flies out of Guantanamo on Tuesdays and Fridays. It’s a regularly scheduled charter flight that flies from Guantanamo Bay, Cuba, to Jacksonville and then continues on to Norfolk, Virginia, said Bill Dougherty, a spokesman for Navy Region Southeast.
Passengers who use this aircraft pay a standard fare for the transportation to and from Guantanamo. The passengers can be military personnel, their families, civilian employees or contractors who work or live at Guantanamo.
"At approximately 9:40 p.m. today, a Boeing 737 arriving from Naval Station Guantanamo Bay, Cuba into Naval Air Station Jacksonville crashed into the St. Johns River at the end of the runway," Naval Air Station Jacksonville said in a statement. "Navy security and emergency response personnel are on the scene and monitoring the situation."
There were thunderstorms in the area during the accident, but an official said it was unclear if that was a contributing factor.
The mayor of Jacksonville, Lenny Curry, earlier tweeted it was a commercial plane, but it was actually a 737 contracted by the Department of Defense. He later said "all lives have been accounted for."
"It think it is a miracle," Capt. Michael Connor, commanding officer for Naval Air Station Jacksonville, said at an overnight press conference. "It could have ended very differently."
Authorities also said teams were working to control jet fuel which had leaked into the water.
The plane skidded off one of two runways at Naval Air Station Jacksonville. The base specializes in anti-submarine warfare and training pilots. It is also home to Naval Hospital Jacksonville.
"To say that I was wiping sweat off my brow would be an understatement," Tom Francis, spokesperson for Jacksonville Fire and Rescue, said in response to the lack of serious injuries.
Curry said he was contacted by President Donald Trump to offer help in the wake of the accident.
Over 80 Jacksonville Fire and Rescue personnel responded to the scene, including members of the hazmat unit.
The National Transportation Safety Board is now investigating the accident.
ABC News' Luis Martinez, Matt Foster and Chris Donato contributed to this report.