Hancock County Emergency Management Director Brian Adam said water stood up to 4 feet deep in many low-lying areas of Hancock County and was still rising as Isaac hovered nearly stationary off the mouth of the Mississippi River.
"It's flooding in quite a bit of places," Adam said before dawn, citing reports from Pearlington, Lakeshore and parts of Waveland and Bay St. Louis.
He said crews successfully rescued three people who had called for help after a houseboat broke loose in Pearlington, near the Louisiana state line but had no major incidents to report immediately. But authorities said they were awaiting daylight to better assess the punch Isaac was delivering to the region.
American Red Cross spokesman Jay Huffstatler said nearly 2,000 people had entered a total of 33 shelters in Mississippi to wait out the storm.
"We've had a great turnout at shelters, people are taking the storm seriously," Huffstatler added.
Hancock County is unusually vulnerable to storm surge because water driven into the Mississippi Sound piles up against the V-shape coast where Louisiana and Mississippi come together. Adam said he wasn't sure if any structures had been damaged. Most buildings destroyed by 2005's Hurricane Katrina in Hancock County were elevated when rebuilt.
In Biloxi, the eastern end of the city, a point that juts into Biloxi Bay where most casinos are located, was being threatened by rising water, authorities said. They cautioned that the high tide wasn't expected until midmorning -- a critical time as Isaac hung off the nearby coast of southeastern Louisiana.
Power outage totals in Mississippi remained below 10,000. Coast Electric Power Association said about 4,000 customers were without power when it called in crews after 10 p.m. because of unsafe conditions. Singing River Electric Power Association also reported about 1,500 customers with the lights out, mostly in Pascagoula.
Pascagoula City Councilman Frank Corder said the power went out at his house after 1 a.m. Wednesday. He said the area had been hit by "occasional gusts and rain, but not too bad so far."
Despite fears that Isaac could dump a deluge on the already soggy Mississippi coast, rain totals have been relatively light so far. Less than an inch had been reported just after midnight Wednesday in Gulfport, Biloxi and Pascagoula.
Winds rose above 20 mph Tuesday afternoon and stayed there through midnight. A gust of 43 mph was recorded at Gulfport-Biloxi International Airport just after midnight, the worst yet recorded there.
The Mississippi Department of Transportation said beachside U.S. 90, a major thoroughfare, was flooding in several locations in Harrison County, though the agency's functioning traffic cameras showed the road to be passable.
Before Isaac reached the coast, Mississippi Gov. Phil Bryant and other officials are warning residents not to get complacent about Isaac. Authorities had warned of the threat of significant flooding even hundreds of miles inland in coming days.
"This is a slow-moving system and we expect heavy rain to occur throughout Mississippi," said Federal Emergency Management Agency Administrator Craig Fugate, speaking Tuesday with Bryant at a Mississippi Air National Guard base in Gulfport. "This is not just a storm for coastal Mississippi."
Isaac made landfall at 6:45 p.m. CDT Tuesday in Plaquemines Parish, La.
As Isaac pushed closer to shore Tuesday, bands of rain pelted the Mississippi coast. Harbors were mostly empty, other than disabled boats that couldn't be moved. In Pass Christian, a sail boat had washed aground near the beach and bobbled in the surf. Many houses were boarded up.
The Mississippi Gaming Commission on Tuesday ordered Harrison County's 10 casinos shut on Tuesday, following the Monday closure of Hancock County's two gambling halls. Many businesses were closed, and postal workers wrapped mailboxes in plastic.