The project would cost between £2 billion and £4 billion and has been submitted to the Department for Transport and the Environment Agency.
The tunnel would be formed by immersing concrete tubes within a trench dredged across the Thames.
Metrotidal director Mark Willingale said: "We propose to fund the tunnel by combining the emerging Government flood defence budget with wholly private-sector funding for the tunnel and tidal power plant.
"A new road connection from the A130 and A13 in Essex to the A289 and M2 in Kent will create a new road orbital system for the whole Thames Gateway region.
"Similarly, a new twin-track rail connection from Wickford and Pitsea in Essex to Rochester and Ebbsfleet in Kent will create a new rail orbital for Thames Gateway that links the eastern limbs of Cross Rail – the new cross London rail system."