Hurricane Nate made landfall in east Gulfport about 12:30 a.m. Sunday, according to the National Weather Service in Jackson.
Earlier predictions had said it would strike land in Pass Christian, Long Beach or Gulfport.
Nate came ashore as a Category 1 hurricane with sustained winds of 85 mph winds.
Light rain and brisk winds were expected across the Mississippi Coast overnight.
Heavy rain and gusty winds had pummeled parts of the Coast for more than nine hours and then began its move toward the Deep South.
Some residents will wake up Sunday to find tree damages, an NWS report from Jackson said.
More than 20,000 homes in the six southernmost counties were without power early Sunday morning.
Nate continues to move north but Jackson County is expecting problems from storm surge into Sunday.
Numerous streets and roads are flooded, said Jackson County Emergency Manager Earl Etheridge, and more flooding is expected.
A tornado watch is in effect for Jackson and George Counties until 2 a.m.
“We’re starting to see some water going down, but that will time some time,” Rupert Lacy, Harrison County emergency manager, said after Nate moved away from the Coast.
“We will do damage assessment at first light.”
The eye, miles long, crossed over Keesler Air Force Base, home of the Hurricane Hunters, the NWS said in an alert.
The National Hurricane Center has confirmed the hurricane made landfall five miles west of Biloxi.