Some 40,000 families have been affected by the flooding, which has isolated many communities near the Amazonian city of Trinidad, the capital of Beni province.
Many of the residents of this area are members of indigenous tribes, some of whom live on the grounds of a national park in the area.
Celso Rocha, whose village has been completely flooded, said that he lost most of his food to the flood waters and animals.
The military´s assistance comes in the form of a 15-day operation to use a large boat to dispatch smaller boats to isolated villages carrying food, much of it donated by the World Food Program.
The Bolivian military´s operation is the first aid many communities in the area have received. Victor Baldivieso, the commander of the Bolivian Navy´s second district, said that some areas have gone three months without any assistance.
Flooding is not new to the area, which has suffered from flooding and intense rains in 2005, 2006, 2007, and 2008. In 2008, the flood waters entered the city of Trinidad itself.