Metropolitan Police officers were alerted to the demonstration at 5.40am.
Four hours later the protesters were removed from the runway and it was reopened at around 12pm.
More than 120 flights were delayed or cancelled after protesters locked themselves together on the airport's single runway.
The accused include William Pettifer, 27, of Radford; Esme Waldron, 23, from Brighton; Natalie Fiennes, 25, and Ben Tippet, 24, of Wandsworth, south London; Deborah Francis-Grayson, 31, from Slough, Berkshire, and Richard Collet-White, 23, from Kempston.
Also charged are Sama Baka, 27, Sam Lund-Harket, 32, and Alex Etchart, 26, of a houseboat on the River Stort in Roydon, Essex.
They have all been released on bail to appear before Westminster Magistrates' Court on 14 September.
London City Airport has been brought to a standstill by Black Lives Matter demonstrators who stormed the runway early this morning to protest against the UK's 'racist climate crisis'.
Incident triggered huge security concerns amid reports demonstrators used a blow-up dinghy to get airside. Only last month they targeted Heathrow Airport.
The demonstrators are part of the British wing of a campaign set up in the US to protest about black Americans being shot by police - although the original branch of the group has never campaigned about climate change.
The Met Police have confirmed seven people have been arrested following the Black Lives Matter protest at London City Airport.
Officers negotiated with the protesters early on Tuesday morning, but at approximately 9.30am officers began making arrests.
In a statement, they said: "So far seven people have been arrested on suspicion of aggravated trespass, being unlawfully airside and breaching London City Airport bylaws."
Of those seven, two have been removed from the runway. All those arrested will be taken to east London police stations.
They added: "Work continues to remove the remaining protesters from the runway".
Wail Qasim, who was at the Heathrow protest, told ITV News: "Since 1990, at least, we've seen zero convictions for over 1,563 deaths in police custody."
The protests have been organised for the day after the anniversary of Mark Duggan's death, which sparked riots nationwide in the summer of 2011.
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