Monday's shutdown affected up to 16,000 passengers who were due to fly from London's fifth-biggest airport, although some airlines switched their flights to the city's other hubs.
In a message sent from its official Twitter account on Sunday evening, the airport had confirmed the discovery of a World War Two bomb in the river at King George V Dock.
London City Airport has reopened to passengers following the disruption and is expected to operate as normal on Tuesday.
A 214m exclusion zone was set up after the German general goal bomb was found grounded in the seabed at King George V Dock in east London.
Lieutenant Commander Jonny Campbell, the officer in charge of Southern Diving Unit 2, said: 'We are taking the necessary steps to ensure the device is as safe as possible before we remove it from the sea bed and tow it away to a safe disposal site.
Residents who were evacuated to temporary accommodation have been told they can return to their homes.
According to its website, 131 flights were scheduled to depart the airport, with a further 130 arrivals.
Flight operations at London City Airport have resumed today, after a 500-kg WW2 explosive device was found during building work nearby yesterday.
It is also close to London's East End which was bombed heavily during the Blitz - Germany's bombing campaign on the United Kingdom during 1940 and 1941.