The device was found at George V Dock during pre-planned work at the airport on Sunday morning.
Properties near the airport were evacuated overnight with residents moved into temporary emergency accommodation.
In a message sent from its official Twitter account on Sunday evening, the airport confirmed the discovery of a World War Two bomb in the river at King George V Dock.
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He said that any passengers expecting to fly to or from the airport today should contact their airline for further information.
City Airport is located in London's Docklands close to the financial heartland of Canary Wharf.
Specialist police officers and the Royal Navy are dealing with the bomb, that is likely one of the thousands of bombs dropped on London by the German Air Forces during the "Blitz" between September 1940 and May 1941.
"A number of road cordons are in place, and motorists planning to travel through this part of Newham borough are urged to seek alternative routes".
Operations to remove the bomb are ongoing. "Good service on the rest of the line".