And officials from the Colombian Institute of Hydrology, Meteorology and Environmental Studies warned residents that the rainy season would continue until mid-June.
Forecasters also predicted that the rains will intensify in the next few days.
Rescue workers in the affected regions have been assisting residents in removing belongings from flooded homes.
"Our situation here is that the river flooded everything. It damaged all the crops - look at the banana plantations - the river also killed my pet," one resident, Guillermo Hernandez, told Reuters.
Others said the flood waters would have long-term repercussions for their livelihoods.
"The crops are all gone because the papaya dies immediately and it takes time for the banana plantations to produce again. Any help that someone could give to us will be welcome," Julio Gonzalez also told Reuters.
On Wednesday the flooding also hit residents in the central and south west provinces of Cundinamarca, Tolima, Valle and Cauca, the government said.
And in the northern city of Baranquilla, residents tied their cars to lampposts and trees to avoid them being swept away by flood waters.
Last year in Colombia heavy rains killed 58 people, injured 111 and left 14 others missing, officials said.