The organisation, which has been working with residents to prepare for floods, further report that many people have been cut off from food supplies and are eating their livestock to survive.
They believe that government and local groups must work together to make sure that communities are able to survive these extreme weather conditions.
Most of Beni province, which is roughly the size of Britain, is under water.
The floods are thought to be part of the El Niño effect, which is being felt all over Bolivia with drought, hail and freezing temperatures in highland areas killing animals and crops.
Recent floods in Mozambique and the Philippines are also linked to El Niño and have affected thousands of people.
Andrew Pendleton, Christian Aid's senior climate change analyst, said: "This is yet again an illustration of how the lives of vulnerable poor people are at the mercy of the weather.
"This El Niño phase gives us a glimpse of what the world might have to cope with as the climate changes invoke greater extremes of weather. It's not a pretty picture."
In eastern Bolivia, the effects of the flooding are made worse by the large scale deforestation of the Amazon basin by large-scale cattle ranching and soya production.
CIPCA has worked in the area for 10 years. Director, Oscar Bazoberry said: "We understand that floods are a characteristic of the area, and that they may get worse because of climate change."
