This paper applies a policy analysis approach to the question of how to effectively regulate micropollution in a sustainable manner. Micropollution is a complex policy problem characterized by a huge number and diversity of chemical substances, as well as various entry paths into the aquatic environment. It challenges traditional water quality management by calling for new technologies in wastewater treatment and behavioral changes in industry, agriculture and civil society. In light of such challenges, the question arises as to how to regulate such a complex phenomenon to ensure water quality is maintained in the future? What can we learn from past experiences in water quality regulation? To answer these questions, policy analysis strongly focuses on the design and choice of policy instruments and the mix of such measures. In this paper, we review instruments commonly used in past water quality regulation. We evaluate their ability to respond to the characteristics of a more recent water quality problem, i.e., micropollution, in a sustainable way. This way, we develop a new framework that integrates both the problem dimension (i.e., causes and effects of a problem) as well as the sustainability dimension (e.g., long-term, cross-sectoral and multi-level) to assess which policy instruments are best suited to regulate micropollution. We thus conclude that sustainability OPEN ACCESS Sustainability 2014, 6 1993 criteria help to identify an appropriate instrument mix of end-of-pipe and source-directed measures to reduce aquatic micropollution.