A second person was injured in Monday's incident when a car crashed into two bus shelters in different parts of the French city. At this point, police are not treating it as terror-related.
At least one person was killed and another injured in Marseille on Monday when a van crashed into two bus shelters in different parts of the French city, police said.
France's counter-terrorism prosecutor said it had not taken up the case at this stage.
Police advised the public to avoid the Old Port area where the driver, a 35-year-old man, was arrested.
A source close to the investigation said the suspect was known to police for minor crimes and had psychological issues.
"The arrest was made in a surprisingly calm fashion, no gunshots were exchanged," David Reverdy, of the Alliance police union in Marseille, told BFM TV.
The driver first hit a bus shelter around 8:15 a.m. (0615 GMT) in the poorer northern part of the city, before ramming into a second one an hour later, several kilometres (miles) to the south.
"The distance travelled by the driver suggests a certain determination," Reverdy said.
"But we can ask ourselves: why these places? If one wanted to cause carnage, other places in Marseille, at another time of day, would have been more logical," he said.
The incident comes as Spanish police hunt for a 22-year-old suspect they believe was behind the wheel of a van that ploughed through crowds in Barcelona on Thursday, killing 13.
France has been under a state of emergency since November 2015 when an attack in Paris killed 130 people in and around the capital in an assault claimed by Daesh.
Daesh also claimed responsibility for an attack in Nice in July last year in which 86 people died when a Tunisian man drove a truck along the seafront boulevard, mowing down Bastille Day revellers.