Officials said Monday's floods followed a day of heavy rains in the town of Bardhere.
Local aid workers said an estimated 12,000 people were made homeless by the floods, which destroyed hundreds of homes and businesses.
They said many of the displaced are living in makeshift shelters in elevated areas around the town.
Officials said water levels in the nearby Jubba river are rising, creating fears of more flooding.
The rains are part of Somalia's short Deyr rainy season which stretches from October to November.