The ferry, operated by transport firm Hadag, was hit in the Tollerort terminal near Hamburg, amid a swell in the River Elbe as Storm Ylenia battered northern Germany with gale force winds.
The film, recorded by a passenger in a seated area at the front, shows the ferry dip suddenly before its windows are engulfed by the wave.
A loud bang can be heard as the water crashes through the smashed window and submerges the floor where passengers are sitting down.
A woman can be heard screaming before other passengers pick up their belongings and escape to another part of the boat.
There were no immediate reports of injuries.
Hadag said in a statement that some of its services have been cancelled due to the high water levels.
Meteorologists are warning Germany could see more extreme weather after a storm that swept across the country overnight on Thursday toppled trees and caused widespread delays to rail and air traffic.
German rail company Deutsche Bahn said it halted long-distance connections in seven northern states early Thursday.
Meanwhile, national carrier Lufthansa and other airlines also cancelled several flights due to Storm Ylenia.
Germany's North Rhine-Westphalia state closed schools as a precaution, and several other states said students could stay home if they wanted.
In Bavaria, trees falling on power lines left more than 10,000 people without electricity.
Meteorologists said they measured winds speed of up to 135 kilometres per hour (84 miles per hour) in low-lying areas.
Germany's national weather service DWD predicts that Storm Zeynep will hit the country on Friday.
Cyclonic weather coming in from the Atlantic is expected to send further storms toward Europe in the coming days.
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