According to the rescue services the motorboat, which had a man and a woman onboard, sank after being split in two by the ferry.
The couple were picked out of the water by other leisure boats and taken to the Gåshaga jetty.
Divers, ambulances, a rescue helicopter and a number of rescue boats were called to the scene. The woman was taken to Karolinska university hospital by helicopter but she was said not to have serious injuries.
Waxholmsbolaget carries 1.8 million passengers a year to Stockholm’s archipelago and has been plying the routes to the east coast islands since 1869.