Gemma McCluskie's limbless torso was discovered floating close to Hackney's Broadway Market after she attended a high-profile hospital opening ceremony in east London last Thursday.
Her 35-year-old brother Tony was formally charged by police on Saturday night as divers continued their searches for Miss McCluskie's remaining body parts.
He will appear in custody at Thames Magistrates' Court today.
Miss McCluskie, 29, who played Kerry Skinner in the BBC soap in 2001, disappeared after attending the opening of the new £650 million Royal London Hospital, in Whitechapel, east London.
She was reported missing to police two days later.
Friends of Miss McCluskie launched extensive searches across east London in a bid to find her.
Former EastEnders co-stars Natalie Cassidy and Brooke Kinsella both appealed on Twitter for help.
Miss McCluskie's remains were discovered on Tuesday when a member of the public reported a suspicious object in Regent's Canal.
A post-mortem examination has proved inconclusive.
Tony McCluskie, of Pelter Street, Hackney, was arrested on Wednesday.
He is accused of killing his sister between February 29 and March 6.
Miss McCluskie's character arrived in Walford as a friend of Zoe Slater and the great-niece of the late Ethel Skinner. She briefly dated Robbie Jackson and got him to propose to her.