The man, 38, was charged for sexually abusing a minor and for recording images of a pornographic nature involving a minor, the source said.
A second soldier who had been detained over the case has been freed without charge.
The two men had been repatriated after being questioned by French and Burkinabe military police in capital Ouagadougou.
Sources close to the Burkina Faso investigation say the two soldiers -- aged 36 and 38 -- met the mother of the youngest girl at the swimming pool on Sunday and were invited to her home for a drink.
One of the two men left behind his GoPro portable camera, on which the mother found the images from the swimming pool which showed the alleged abuse, a source said.
The mother took the "fairly long" film to the French embassy, and it was later seen by the father of the other child.