Isaac dumped as much as 16 inches of rain in some areas, and about 500 people had to be rescued by boat or high-water vehicles.
At least five deaths were reported in Louisiana and Mississippi.
The latest two victims, a man and a woman, were discovered late Thursday in a home in the hard-hit town of Braithwaite, south of New Orleans. Authorities said deputies went to search for the couple after someone reported they had apparently not escaped the flooding. Their names were not immediately released.
An unidentified man died in a restaurant blaze in Gretna that firefighters could not control because of Isaac's strong winds Wednesday. Another man died falling from a tree during the storm and a tow truck driver in Mississippi was killed when a tree crushed the cab of his truck.
On Grand Isle, a barrier island on the Gulf, the town pumped away water. Sections of the only road to town had washed out.
On a street turned river in Reserve, on the east bank of the Mississippi River, two young men ferried their neighbors to the highway in a johnboat, using boards as paddles.
Lucien Chopin, 29, was last to leave his house, waiting until his wife and three kids, ages 7, 5 and 1 were safely away.
He was finally joining them late Thursday, hoping they would find a shelter.
His van was underwater and water flowed waist-high in the house he'd rented for eight months.
"It's like, everything is down the drain. I lost everything. I've gotta start all over."
Chopin was upset that pumps meant to keep the area dry either failed or were shut off.
"We knew it was coming, but they didn't tell us we had to evacuate. We had no idea it was gonna be like this," he said, a refrain echoed by many.
Cisco Gonzales, a heating and air conditioning business owner, said he got his boat and truck and headed for higher ground when he heard the water was rising quickly, from 0 to 6 feet of water in five minutes.
"I've never seen so much water in my life," said Gonzales, who built a home in Braithwaite, southeast of the city, after his previous home was damaged by Katrina in 2005.
He rode out the storm at a ferry landing and when the weather calmed, he went out and rescued about a dozen people.