The groundwater quality recovery within a polluted aquifer system is often un-ideal as there are lots of uncertainty factors. These uncertainty factors may be classified two groups. One is of objectivity, which is concerned with heterogeneity of aquifer media; non-equilibrium desorption of pollutants; non-uniformity of adsorption distribution coefficient; pollutants with non-aqueous phase liquids; a partial well and its effect on flow behavior in the pump-and-treat system. Another is of subjectivity that is concerned with setting up the model, determination of some hydraulic parameters and others. Finally, it is mentioned that some steps, i.e. definition of the problem, uncertainty analysis and risk-assessment, should be involved as an effective analysis method.