The 2004 Olympic 400 metres freestyle champion, who quit swimming in 2009 after becoming pregnant, returned to the sport last year in an attempt to qualify for the London Games.
She clocked 1:00.42 in the heats and then 1:00.58 in the semi-finals, under the required 1:00.82.
Manaudou will need to finish in the top two in Tuesday's final with a time under the Olympic A qualification mark.
"I started strong and I struggled a bit towards the end," Manaudou told reporters after her semi-final.
Camille Muffat looked impressive in the 400 metres freestyle final as she set the fastest time in the world this year of 4:01.13 to qualify for the Olympics.