We have studied charged nuclear fragments produced by 200 -400 MeV/nucleon carbon ions, interacting with water and polycarbonate, using a newly developed emulsion detector. Total and partial charge-changing cross sections for the production of B, Be, and Li fragments were measured and compared with both previously published measurements, and model predictions. This study is of importance for validating and improving carbon ion therapy treatment planning systems, and for estimating the radiological risks for personnel on space missions, since carbon is a significant component of the Galactic Cosmic Rays. PACS numbers: 25.70.Mn,