It has been raining for much of the week, but a weather system connected to Hurricane Joaquin in the Caribbean is expected to make the situation worse.
It is regaining strength and has been reclassified as a Category 4 Storm.
Hurricane Joaquin, currently off the Bahamas, has winds of up to 155mph.
The storm is not expected to hit the eastern US, but the moisture associated with it is contributing to heavy rainfall, particularly in South Carolina.
The National Weather Service says parts of the state could see over 15 inches of rain by Sunday evening, October 4.
In the historic city centre of Charleston, many streets have been closed and sandbags have been piled up to keep floodwaters out.
“Where we normally are dealing with flooding for a few hours, we’re dealing with it in days here,” Charleston Police Chief Greg Mullen told the Associated Press.
The emergency declared by President Barack Obama means state and local authorities can receive federal help to deal with the flooding.
On October 1, El Faro cargo ship went missing after sailing through Hurricane Joaquin off the Bahamas.
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