The driver of the Ulsterbus sustained minor injuries in the incident, which happened on the Portaferry Road at about 06:30 GMT on Wednesday.
Translink said no passengers were on board the bus and no other vehicles were involved.
It said the driver had been taken to hospital to be assessed and an investigation was ongoing.
"PSNI attended the scene," a Translink spokesperson said.
A  major operation to recover the bus from the water has now ended.
Councillor Kellie Armstrong said her husband, Barry, who is deputy station officer with Portaferry coastguard, was called to the scene on Wednesday morning.
She said the driver of the bus was fortunate he did not sustain more serious injuries.
"I came past the scene on my commute to work this morning," she said.
"There is a substantial chunk out of the wall on the passenger side.
"The bus driver is lucky he did not sustain worse injuries, and was not thrown through the front window.
"It was windy and dark this morning, the tide was out at the time of the incident and it is lucky the tide was not in or the bus would have been submerged."
Councillor Armstrong said the removal process was hampered by the incoming tide later in the day.
"The tide came in and that made everything more complicated. The conditions were difficult for those involved in the removal."
A bus that crashed onto a beach near Newtownards, County Down, has been removed.