Many voices call for better transboundary coordination and management of ecological networks. Little, though, is known about the kind of transboundary cooperation currently going on in establishing ecological networks across European borders. The objective of the present research is to gain an empirical overview of transboundary cooperation in establishing ecological networks on Germany's external borders, to analyse reasons why such cooperation is launched and why some border regions seem to be more active in this than others, and finally to identify shortfalls in current practice and potential remedies. The empirical analysis is guided by a theoretic framework which includes hypotheses on: (1) the institutional context, (2) structural and situational contexts, (3) actors with their resources, orientations and interests, (4) actor constellations, and (5) ideas, symbols and discourses. The methodology consists of a literature review, a comprehensive internet survey in combination with exploratory expert interviews, and a series of semi-structured, open-ended, in-depth interviews. We identified 34 transboundary cooperation projects in establishing ecological networks across Germany's external borders in the period 2003–2007, the majority of which was located at Germany's western borders. Many factors that had been derived theoretically were borne out by the interviews. However, hypotheses on the influence of NGOs and on international institutions and organisations seem to be of specific explanatory value. In practical terms we recommend intensifying the flow of knowledge and information between practitioners in this field and strengthening the ties between ecological network planning and spatial planning in transboundary contexts.