New Orleans could experience 6 to 9 feet of storm surge, Mayor Mitch Landrieu said midday Saturday, citing National Weather Service predictions.
A dozen casinos in MS took the rare step of closing early as the storm moved in.
Earlier Sunday, Nate came ashore outside Biloxi, Mississippi, as a hurricane, the first the make a direct hit on the state since Hurricane Katrina in 2005.
The storm, with maximum sustained winds of 137 kmph, is moving north, and a second landfall is expected on the MS coast later, BBC reported on Sunday.
Hurricane warnings for metropolitan New Orleans and Lake Pontchartrain were downgraded to tropical storm warnings, according to the hurricane center.
More than 100,000 residents in MS and Alabama are without power following the arrival of Nate.
The storm's track and asymmetrical shape, with its highest winds and heavy rain on its east side, could spare New Orleans from any real damage, Watson said.
A state of emergency was also declared for 29 Florida counties. The platforms mostly avoided Hurricane Harvey in late August.
Emergencies declared in Mississippi, Louisiana. And its quick speed lessened the likelihood of prolonged rain that would tax the city's weakened drainage pump system.
Cities along the MS coast such as Gulfport and Biloxi were on high alert.
Curfews are in place and evacuations called for in beachfront and flood-prone areas. About 2,000 people were affected.
The Storm Surge Warning has been discontinued west of Grand Isle.
A number of Central American countries have felt the full force of Nate, at the time a tropical storm, as it made its way north.
"Strengthening now appears unlikely before Nate's center reaches the MS coast", the hurricane center said in a bulletin.
The storm was located about (555.2 kilometres) south-southeast of the mouth of the Mississippi River and was moving north-northwest at 22 miles per hour (35 kph). The hurricane is bringing severe weather with it - tornado warnings have been issued for parts of Alabama. Based on the current track, the likelihood of seeing tropical-storm-force winds in excess of 40 miles per hour is possible in or near metro Atlanta from Nate is increasing.
"I think that you saw a team of people, both on the federal, state, and local level, get in a position of preparedness that I think is very very admirable", Landrieu said.
Tropical-storm-force wind gusts are expected over the the Florida Panhandle, and portions of Alabama and Georgia through on Sunday, the NHC said.
Nate has brought stinging rain to the Gulf Coast and its powerful winds have pushed water onto roads.
The storm will be the third hurricane to hit the continental US, the first time that's happened since Gustav, Dolly and Ike struck in 2008, said Phil Klotzbach, hurricane researcher at Colorado State University. Other voluntary evacuations were issued for parts of Lafourche and St. John parishes, WWL-TV also said.
The hurricane's center continued to cross inland across the Deep South, Tennessee Valley, and central Appalachian Mountains through Monday.
Officials warned coastal communities of the storm surge, which is the height of water above dry ground.
According to Okaloosa County EOC officials they are anticipating the storm surge to be between two and four feet.