Rescue services at the scene near the village of Mepal in Cambridgeshire tried to rescue him by smashing the glass of the cab. They lifted his head out of the water but his leg was trapped.
Heavy lifting equipment was brought in to lift the crane and its operator out of the water but time ran out and the man was unable to survive the icy temperature.
The operator, an Environment Agency employee dredging the Old Bedford river, was declared dead at around 1pm, some three hours after the crane fell in.
Julian Fountain, incident commander for Cambridgeshire Fire & Rescue Service, said: "All agencies have worked extremely closely together to make every effort to fully release the man from the water as quickly as possible.
"However, due to the location of the crane, the freezing weather conditions and the fact that the man was trapped, this could not happen in time.
"This is an extremely tragic incident. Our thoughts go out to the man's family."
Both the Environment Agency and the Health & Safety Executive are investigating.