Flooding is reported to have hit several areas outside Santa Cruz. In El Torno, southwest of the city, residents have been forced to climb onto the roofs of their homes or into trees to escape the waters.
Helicopters have been deployed in the rescue operation.
President Rodrigo Paz called an emergency meeting this weekend where he warned that Bolivia is facing a difficult situation due to the weather phenomena La Niña and El Niño.
During the first days of the rainy season, all reported records from the last 100 years have been broken, Paz said.
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