Rivers and streams including Río Botello overflowed from around 04:00, flooding neighbourhoods such as Los Manzanos and La Selva.
Residents reported water levels exceeding 1 metre inside homes, while at least 14 incidents were recorded across Cundinamarca, governor Jorge Emilio Rey said.
Emergency services including the fire department, police and the Red Cross deployed pumps and evacuation teams throughout the day.
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More than 1,000 people were moved to temporary shelters, where food and basic supplies were distributed.
The national weather agency IDEAM warned further rainfall could hit the region in the coming days, increasing the risk of landslides in nearby Andean areas already weakened by saturated ground.
