Emergency services have told the source they are searching for the couple and several other missing people.
People in central Greece were trapped on the roofs of their houses after floods set whole villages under water.
More than a dozen people are now known to have died since Storm Daniel hit Greece, Turkey and Bulgaria this week.
The Austrian couple decided to shelter inside the bungalow they had rented for their honeymoon as heavy rainfall swept central Greece, the owner of the accommodation, Samaras Thanakis said.
But the house in the beach resort of Potistika, near Mount Pelion, was then washed into the sea by flash floods, he told the BBC.
He and other guests had left for higher ground and had advised the couple to do the same.
“The situation was very bad. It’s very difficult to decide what to do in a moment like that,” Mr Thanakis said.
He added that the couple, from the Austrian city of Graz, had married shortly after arriving on their holiday.
The Greek fire brigade said it had a team in the area searching for missing people, including the newlyweds.
Some Greek regions received up to 800mm (31.5 inches) of rain in recent days – more than normally seen in a whole year.
The Karditsa plain in central Greece was described as having turned into a lake, with villages around Palamas drowned in water.
The mayor of Palamas, Giorgos Sakellariou, made a dramatic appeal for help on Greek TV, saying people were stranded in their homes and facing immediate danger.
“The situation in Palamas is tragic,” he was quoted as telling Skai TV. “People are trapped in their houses. We will have people drowning.”
Rescue efforts have been hampered after several bridges in the region collapsed and roads were seriously damaged
The extreme weather also hit Athens and the island of Skiathos, where thousands of tourists remain stranded, as well as coastal areas around Volos and Pelion.
Prime Minister Kyriakos Mitsotakis cancelled a big government engagement planned for the weekend as the crisis escalated.
Storm Daniel has been hitting Greece, Turkey and Bulgaria since Monday, with more than a dozen people known to have died, at least four of them in Greece.
Climate scientists have warned that global warming means more water evaporating during the summer, leading to more intense storms.
Source BBC News
