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The comedian is reportedly taking refuge in a hotel while the damage is repaired.
Water is said to have cascaded through the kitchen of his five-bedroom converted pub home, which he shares with girlfriend Roxy Hormer, 29.
His dining room was reportedly destroyed during the flood which caused chaos and left a trail of destruction across London last week.
Whitehall, 33, bought the property last month.
A source told the Sun: “He’s gutted. Talk about putting a dampener on moving in. The house is incredible and he loves it. There’s even a lift and swimming pool in it. He wasn’t expecting the kitchen to become a pool as well.
"It has loads of bedrooms and a nice outdoor space. "The courtyard is enclosed at the back and it started to flood very quickly. “The rain was unbelievable and just didn’t stop coming.
“It started to flood into the back of the house, it came into the kitchen.”
Flood waters poured through the streets and seeped into homes, shops and restaurants on Notting Hill’s Portobello Market when a month’s rain hit the capital in just 90 minutes on Monday July 12.
London Fire Brigade received thousands of calls and rescue teams evacuated properties amid fears of collapsing ceilings.
Kensington and Chelsea council is offering support to residents affected by the floods.
A spokesman said: “All affected tenants who required accommodation were helped from their homes into safe accommodation.
“Council officers are attending on site as quickly as possible to help with the clean-up of premises.”