A military-chartered jet carrying 143 people landed hard, then bounced and swerved as the pilot struggled to control it amid thunder and lightning, ultimately skidding off the runway and coming to a crashing halt in a river at Naval Air Station Jacksonville, Florida.

It meant chaos and terror for passengers in the Boeing 737, as the plane jolted back and forth and oxygen masks deployed, then overhead bins opened sending contents spilling out.

But authorities said everyone on board emerged without critical injuries Friday night, lining up on the wings as they waited to be rescued.

The U.S. National Transportation Safety Board (NTSB) sent a team of investigators Saturday to the crash site in the St. John's River in north Florida, where the aircraft was still partially submerged in shallow water and its nose cone was sliced off, apparently from the impact.

Several pets were still on the plane as well, and their status wasn't immediately clear. A Navy statement early Saturday offering "hearts and prayers" to their owners said safety issues prevented rescuers from immediately retrieving the animals.

Flight came from Guantanamo Bay, Cuba

The flight took off Friday from the U.S. military base in Cuba with 136 passengers and seven crew members. It was a regular charter run by Miami Air International, which has many military contracts, including weekly flights between the Naval Station Guantanamo Bay, Cuba, and the Jacksonville air station as well as Andrews Air Force Base in Maryland. The company didn't immediately respond to messages from The Associated Press.

A Boeing 737 plane arriving from Guantanamo Bay in Cuba went off the Naval Air Station Jacksonville runway in Florida and into the St. Johns River on Friday night. (CBC)

Among those onboard was Cheryl Bormann, a defence attorney, who described the chaotic landing.

The plane "literally hit the ground and then it bounced. It was clear that the pilot did not have complete control of the plane because it bounced some more, it swerved and tilted left and right," she told CNN. "The pilot was trying to control it but couldn't, and then all of a sudden it smashed into something."

Passengers lined up on the plane's wings before climbing into rescue boats, said the base's fire chief, Mark Brusoe.

Bormann said people weren't screaming because the flight staff worked quickly to give direction. Everyone onboard helped one another to put on their life vests and then evacuated to safety.

Watch: Daytime images emerge of a Boeing 737 in Florida river

New daytime images emerge of a Boeing 737 that slid off a runway into a Florida river. 1:01

A veteran death penalty attorney from Chicago, Bormann has been defending Walid bin Attash, who is charged with helping to train some of the 9/11 hijackers. The U.S. holds 40 men at the detention centre at Guantanamo Bay. It has been prosecuting some of them by military commissions, including five charged with planning and aiding the Sept. 11, 2001, terrorist attacks. Their cases have been in the pretrial stage since May 2012 and no trial has been scheduled.

Authorities say everyone onboard the flight was alive and accounted for, but nearly two dozen people were taken to local hospitals. Most have since been released.

Capt. Michael Connor, the commanding officer of NAS Jacksonville, said the passengers were a mix of military personnel and families, and a few civilians. While some were staying in the area, others planned to fly on to other parts of the country.

"I think it is a miracle," Connor said Friday night. "We could be talking about a different story this evening."

Flight data recorder recovered

It wasn't immediately clear what went wrong. Boeing said in a tweet Friday night that it was investigating: "We are aware of an incident in Jacksonville, Fla., and are gathering information." The Federal Aviation Administration was referring media inquiries to NAS Jacksonville. The National Transportation Safety Board dispatched a team of 16 investigators to determine what happened.

Team members recovered the plane's flight data recorder Saturday.

Connor said he didn't know what impact the weather had on the flight. "I was at home when this happened and there were thunderstorms and lightning," he said.

The plane had been expected to return to Cuba on Saturday to carry other members of the military, lawyers and others to Andrews after this week's military commission hearings of people charged with war crimes.

The plane was carrying 136 passengers and seven crew when it ended up in the river. (Monica R. Hopper/U.S. Navy via AP)

It wasn't immediately clear how long it would take to remove the plane from the river. Connor said the landing gear appeared to be resting on the riverbed, making it unlikely for the aircraft to float away. He said crews began working to contain any jet fuel leaks almost immediately after securing the passengers' safety.

The smell of fuel and oil was pungent as AP journalists went by boat for a closer look. The bottom of the plane was under water, making it difficult to access the cargo hold.

"We're obviously very concerned about the environment and we're doing everything we can to contain it," Connor said about the fuel. "Once we were assured that personnel were safe, our next priority effort was to ... contain any type of fuel."

Jacksonville Fire and Rescue tweeted that approximately 90 personnel responded to the scene, and that the department's special operations team had just trained with marine units for such an incident earlier Friday.