"I think it is a miracle," said Captain Michael Connor, the base's commanding officer, hours after the plane landed.
"We could be talking about a different story this evening."
The National Transportation Safety Board sent a team of investigators to the crash site in the St Johns 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.
Two pet cats and a dog were still on the plane as well, and their status wasn't immediately clear.
Rescuers looked in the cargo area after the plane ended up in the river but saw no crates and heard no animal noises. When they returned later, they didn't see any pet carriers above water, Connor said.
Members of the 16-person NTSB team recovered the plane's flight data recorder.
Investigators will examine the aircraft, the environment and human factors in trying to discover why the plane rolled into the river. The pavement on the runway wasn't grooved, and Landsberg said grooves can help the water flow off the pavement more quickly. He said investigators will examine what role that may have, with reported heavy rain during the landing.
The flight took off from the US 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 AP.
The aircraft had no prior history of accidents, said NTSB vice-chairman Bruce Landsberg.
Among those onboard was Cheryl Bormann, a defence lawyer, 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."
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.
A veteran death penalty lawyer from Chicago, Bormann has been defending Walid bin Attash, who is charged with helping to train some of the 9/11 hijackers.
The US 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 September 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 sought medical attention.
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, Connor said.
It wasn't immediately clear what went wrong. Boeing said that it was investigating.
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.
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.
- AP
