This study applies the export coefficient and natural breaks classification methods to assess the spatial variability of pollution potential in the Taipei Water Specific Area (TWSA). This work divides the TWSA into twenty-two subwatersheds based on digital elevation data, among which there are six subwatersheds with grade A pollution potential which is the highest level. Stricter land-use policy should be implemented in subwatersheds with larger pollution potential. If these subwatersheds implement land-use management strategies and change 50% of farmlands and 50% of built-up areas to forested areas, the number of subwatersheds with grade A pollution potential can be reduced from six to two. The land-use management strategies addressed in this study can be useful for classifying land-use restrictions in the TWSA.