Stress fractures are caused by the repetitive application of a greater amount of force than the bones of your feet and lower legs normally bear. This force causes an imbalance between the resorption and growth of bone, both of which go on all the time. Repetitive force promotes the turnover of bone cells, but you add new bone cells when you're at rest.
If your bones are subjected to unaccustomed force without enough time for recovery, you'll resorb bone cells faster than you can replace them. As a result, you develop "bone fatigue." Continued, repetitive force causes tiny cracks in fatigued bones. These cracks progress to become stress fractures.
Source: http://www.mayoclinic.com