In Japan, environmental water quality standards for total zinc were established in 2003 for the protection of aquatic life. Further, the Japanese Ministry of the Environment enforced the effluent standard for Zn (i.e., permitted concentration was lowered from 5 mg/L to 2 mg/L) for the maintenance and achievement of the environmental standards. In this paper, the issues on these standards were discussed and the gaps between the objectives and setting procedures of the two standards in the decision making processes were identified. Subsequently, several suggestions, such as performing ex-post evaluations on the regulations of zinc in terms of their influence on the protection of aquatic organisms, were made in order to confirm and fill the gaps.