The purpose of this study is to examine the system of water pollution fees in Taiwan. In order to achieve this objective, we first presented the possible scenarios of fee structure, including fee rates and financial subsidy in Taiwan. Then, a benefit and cost analysis was established to investigate the impacts of scenarios. The criterions behind the study are economic efficiency, fairness, administrative feasibility, and acceptance. We used the water pollution data of Taiwan Environmental Protection Agency (TEPA) to analyze the abatement costs of water pollution in Taiwan. In addition, we discussed the feasibility of setting different fee rates according the different abatement costs or benefits. Finally, we suggested the possible procedures of collecting the fees and assisted the conference meetings for TEPA.