Forecasters warned that Isidore, which devastated Mexico's Yucatan Peninsula, could hit land again near the city of New Orleans by early Thursday.
Around 8,000 people in the low-lying Louisiana communities of Jean Lafitte, Barataria, Crown Point and Grand Isle have been evacuated.
A hurricane watch is in force in the two states, and a less severe tropical storm warning covers areas either side stretching from eastern Texas to western Florida.
However, Tropical Storm Lili - which had threatened Cuba and the island of Hispaniola - appeared to be losing much of its force.
Lili caused widespread damage in the island states of Barbados, St Vincent and the Grenadines, and Trinidad and Tobago earlier in the week.
Mexico damage
As Isidore swept across the Gulf of Mexico, US and Mexican oil companies evacuated thousands of workers from oil platforms. The gulf accounts for about 25% of all US crude oil and natural gas production.
The US National Hurricane Center warned people in Louisiana, Texas, Mississippi and Alabama, and in the area in the north-west of Florida known as the Panhandle, to stay inside and listen to the radio for storm warnings.
Hurricane Isidore smashed into Mexico's south-eastern Yucatan peninsula on Monday, killing at least three people. It has also caused devastation in Guatemala, Nicaragua and Cuba.
The storm uprooted trees, ripped roofs off houses and left about 300,000 people homeless.
Parts of the historic state capital, Merida, were left without power as winds of up to 180 km/h (110 mph) cut off phone lines and whipped up clouds of debris.
People are now anxious to return home, but authorities have not yet declared the area safe.
"We want to go home and see what happened to our house," 45-year-old Bernarda Naal from the coastal village of Chuburna told the Associated Press news agency. "I want to see if I still have a house."
Authorities said one person was electrocuted by downed power lines in Merida, another died of a heart attack as a direct result of the storm, and a third was killed in a car accident outside the city.
Mexican President Vicente Fox, who went to survey the damage, said: "Really there is a lot, a lot of problems and very extensive damage. We will do all that we can to help, and we will do it as fast as we can."
The government has pledged five million pesos ($500,000) to help people rebuild.