Fracking for natural gas and oil is like anything — if it is not done right, problems arise. A good article on this is in the Wall Street Journal
This article indicates that if done right a fracking well will not cause water pollution. There is a good diagram in this article that shows why this is true. I have personally seen presentations with similar diagrams and shows that the actually tracking occurs miles below the surface well away from where the well water is. This well water is at a very shallow depth and is far away from where the tracking occurs. However if the well is not cemented properly and uses three interlocking pipes as this article points out, trouble can result and groundwater can be polluted with the natural gas. All wells should have this design with good cementing.