The Bodoquero River (Spanish: El río Bodoquero) is one of the most important rivers in the Colombian municipality of Florencia, Colombia in the department of Caquetá.

It serves as a natural boundary between the municipalities of Florencia and Morelia and is part of the Amazon River basin.

The Bodoquero River rises in the Eastern Cordillera mountain range (also known as the "Colombian Andes") southwest of the municipal seat of Florencia.

Its waters meander through the territory in a north–south-easterly direction, finally flowing into the Orteguaza River, near the municipality of Milan.

[1] Rivers in this region are often accompanied by the presence of shifting Oxbow lakes.