Earlier, a significant storm surge or rise in ocean waters above normally dry land had affected the area from the Mississippi-Alabama border to the Okaloosa/Walton County line in Florida.
Locally, southerly winds will remain below tropical storm force, but will average about 10-20 miles per hour, and slightly higher at the coast.
The storm's centre will move inland over MS and across the Deep South, Tennessee Valley and Central Appalachian Mountains through today.
The president has already approved an emergency declaration for a large area of Louisiana.
As Hurricane Nate has reached the US Gulf coast leaving almost 100,000 people in the states of Alabama and MS with no power, the US president approved the Alabama governor's request to provide assistance to the state.
The landfall on Sunday was Nate's second.
Thousands were forced to evacuate their homes and Costa Rica's government declared a state of emergency. Officials in Gulf Shores and Orange Beach say their cities are "open and clear".
The Storm Surge Warning has been discontinued west of Grand Isle.
It is expected to weaken at at a rapid rate throughout the day.
Nate claimed the lives of 11 people there and more than 11,000 people are now homeless.
Louisiana Gov. John Bel Edwards encouraged residents to prepare for Nate as if it were a much stronger storm.
Some East Alabama counties are being trimmed out of the Tropical Storm Watch, but there is a Wind Advisory until 10 p.m. CT Sunday for all of the Alabama counties in the WTVM viewing area.