One major challenge faced in environmental management is to adapt the spatial scale of regulation to specific environmental problems. From a natural science perspective, the appropriate scale of management units can be defined by the spatial boundaries within which physical, chemical or biological processes have an environmental effect. However, actual political management units rarely match these ideal states. This is particularly true for transboundary water pollution in general, and micropollution regulation in particular, where different jurisdictions tend to produce diverse policy solutions and implement divergent instruments to tackle identical problems within the same hydrological catchment area. Integrated Water Management strategies and collaborative management modes were developed precisely to meet this challenge, but the question of what the appropriate scale of pollution management is, still remains: How can thepotential mismatch between the physical extent of pollution and the respective political areas of action and regulation towards micropollution be determined, visualized and explained in order to design effective and efficient micropollution regulation? Although a variety of disciplines mention the socio-ecological inter-linkage, they rarely adopt a de facto interdisciplinary approach in which regulatory issues are brought together with the natural-scientific analysis. The research project fills this gap by analyzing the complex issues of water quality management and micropollutants combining natural science, political science and political geography. We specifically investigate the physical spatial extent of the impairment of water bodies caused by micropollutants. This physical space is then compared to the established territorial jurisdictions regulating micropollution and water quality. The main research questions are: how can the potential mismatch between physical and jurisdictional/political areas be identified and understood; and what conclusions can be drawn for the development of future micropollution management and regulation? Some of the major underlying hypotheses state that coordinated policy instrument selection is facilitated when actors from different jurisdictions or countries are similarly affected by micropollution, when they participate within the same transboundary water bodies, or when border effects are reduced through collaborative management strategies. We undertake five tasks; the first two are of a disciplinary character, whilst the last three are interdisciplinary, and an integrated approach is developed to produce interdisciplinary methods and outcomes. In task 1, the physical spatial extent of micropollution is identified through mass flow analysis using Geographic Information System (GIS); in task 2, current EU, national, and sub-national legislation to regulate micropollution is analysed, and policy processes are translated into networks (actors and ties) through a formal social network analysis. In task 3, policy networks are geo-referenced in space to delimit the spatial extent of micropollution regulation from the EU to the national and subnational levels using GIS. The results from tasks 1, 2 and 3 are brought together in task 4: the influence of physical impact zones (areas with strong potential for micropollution), policy process characteristics (such as actors’ relational profiles and political competences), and spatial factors (such as the territorial location of involved actors and border effects) on actors’ preferences for policy instruments regulating micropollution is then assessed. This leads to conclusions about the potential for coordinated policy instrument selection to regulate micropollution in a specific river catchment area.