Police said they were operating on the assumption Colby, 76, had fallen victim to a boating accident and not foul play, although the possibility of violence could not be ruled out.
In any case, his sudden, mysterious disappearance stirred inevitable reminders of the espionage netherworld he once dominated as chief of the CIA from September 1973 to January 1976.
The coastguard said it had received a call from a neighbour of Colby's at about 7.30pm on Sunday, reporting him overdue after a canoe trip that he began on Saturday night.
Authorities in Charles County, Maryland, said Colby had planned to be away only briefly and had left his radio and computer on when he went out.
At least a dozen divers plumbed the depths and combed the shores of the Potomac River and its Wicomico tributary close to where Colby's overturned green canoe was found by a local boater at noon on Sunday.
Officials in Charles County, where Colby had a home facing Cobb Island, said they had no reason to suspect foul play.
"Right now we're viewing it as an accident." said Sheriff Fred Davis. "But I will not rule out foul play. You never rule that out until you finally locate the individual and get an autopsy done. But right now it is being considered as an accident, a boating accident."
Colby, who parachuted into German-occupied France in 1944, went on to mastermind many of the CIA's clandestine operations in Indochina as head of its Far East Division from 1963 to 1968. But he is perhaps best known for having blown the whistle on abuses of CIA power shortly after President Richard Nixon appointed him as director in May 1973.
At that time, he turned over to Congress the CIA's so-called "family jewels" - records of questionable operations that included the unauthorised opening of Americans' mail, illegal domestic phone tapping and psychedelic drug experiments on unwitting Americans.
In his 1978 memoirs, Honorable Men: My Life in the CIA Colby wrote: "The perfect [secret] operator is the traditional grey man, so inconspicuous that he can never catch the waiter's eye in a restaurant."