In the early 2000's, Gonaïves was the scene of substantial rioting and violence primarily motivated by opposition to President Jean-Bertrand Aristide, and on February 5, 2004, a group calling itself the Revolutionary Artibonite Resistance Front seized control of the city, starting the 2004 Haïti rebellion. But in recent years the city has seen a complete return to calmness.

In September 2004, Hurricane Jeanne caused major flooding and mudslides in the city. 3,006 people were confirmed dead in Haïti, and the death toll in Gonaïves was believed to have topped 2,000. Every building in the city was damaged by the storm and 250,000 people were left homeless.

Four years later, the city was again devastated by another storm, Hurricane Hanna, which killed 529 people, mostly in flooded sections of Gonaïves, where the destruction was described as "catastrophic" and 495 bodies were discovered as of late on September 5. [2][3] Haitian authorities said the tally could grow once officials are able to make their way through Gonaïves. "The assessment is only partial, because it is impossible to enter the city for the moment", Gonaïves Mayor Stephen Moise said. At least 48,000 people from the Gonaïves areas were forced into shelters. Some people slept on the roofs of their houses to protect them from possible looters. The catastrophe left many homeless begging for food and clothes. Others left for the mountains hoping to wait out the next storms on the horizon