Police said it happened in the area between the recreation center and Southgate Village Apartments shortly after 2 p.m.
The teen was found shot when officers arrived on the scene and is being treated at a nearby hospital.
Officers believe this was 'an isolated incident' and posed no threat to nearby residents.
Police said the 16-year-old was arrested for aggravated assault with a deadly weapon.
The case remains under investigation and officers are encouraging anyone with information regarding this incident to call the College Station Police Department at (979) 764-3600.