The Bridgeport-Port Jefferson Ferry is back on schedule after a threatening call came in to 911.
One ferry was already en route when the call came in.
Bridgeport police say the Coast Guard was on board to assure the safety of the passengers.
The two remaining boats docked in Connecticut and Long Island were evacuated and searched.
Police say nothing was found and the ferries went back to making their trips.
The nature of the threat was not immediately known.