The present paper describes the planning and implementation of a best management practice (BMP) system for a clay mining facility in Northern Taiwan. It is a challenge to plan and design BMPs for mitigating the impact of clay mining operations due to the fact that clay mining drainage typically contains very high concentrations of suspended solids (SS), Fe-ions, and [H+] concentrations. In the present study, a field monitoring effort was conducted to collect data for runoff quality and quantity from a clay mining area in Northern Taiwan. A BMP system including holding ponds connected in series was designed and implemented and its pollutant removal performance was assessed. The assessment was based on mass balance computations and an analysis of the relationship between BMP design parameters such as pond depth, detention time, surface loading rate, etc. and the pollutant removal efficiency. Field sampling results showed that the surface-loading rate is exponential related to the removing rate. The results provide the basis for a more comprehensive and efficient BMP implementation plan for clay mining operations.