The area stretching from the US capital north to Baltimore is facing "the biggest tidal flood events of the past 10-20 years," the National Weather Service said.
It said that in some areas the damage could be the worst since that caused by Hurricane Isabel in 2003.
"Tidal flooding, strong winds, and severe thunderstorms capable of producing damaging wind gusts and localized rainfall flooding will impact the region," the local office of the NWS said.
Coastal flooding alerts have been issued from the state of Virginia all the way north to New Jersey.
In the Maryland state capital, Annapolis, located an hour's drive from Washington on the Chesapeake Bay, the water came up to people's knees. At least one man used a kayak to navigate the inundated streets.
Sand bags were posted outside stores to keep the water out.
On Monday, California was hit by torrential rain that caused several floods, after months of drought and repeated forest fires.
Climate change is regularly blamed for causing extreme weather events.
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