Police are investigating reports that Acar was a former army sergeant.
Dogan news agency said Acar was discharged from the military in 2002 for disciplinary reasons, but did not provide details.
Television footage showed the man shouting, "I did it for the country", as he was being led away from the ferry to a police vehicle.
Dink had spoken out about the mass killings of Armenians in the early 20th century and had received a six-month suspended sentence in October for "insulting Turkishness".
Tens of thousands of people filled the streets of Istanbul for his funeral, many chanting slogans such as "We are all Armenians" and "Shoulder to shoulder against fascism".
Unemployed secondary school graduate Ogun Samast, 17, has admitted to shooting Dink as the journalist left the offices of his newspaper, Agos, in Istanbul on January 19.