This article explores the value of the Systems Approach Framework (SAF) as a tool for the transition to sustainable development in coastal zone systems, based on 18 study sites in Europe, where the SAF was developed and tested. The knowledge gained from these experiments concerns the practical aspects of (a) governance in terms of policy effectiveness, (b) sustainability science in terms of applying transdisciplinary science to social–ecological problems, and (c) simulation analysis in terms of quantifying dysfunctions in complex systems. This new knowledge can help broaden our perspectives on how research can be changed to better serve society. The infusion of systems thinking into research and policy making leads to a preference for multi-issue instead of single-issue studies, an expansion from static to dynamic indicators, an understanding of the boundaries between system-dependent and system-independent problems, and the inclusion of non-market evaluations. It also develops a real partnership among research, management, and stakeholders to establish a quantitative basis for collaborative decision making. Furthermore, the article argues that the transition to sustainable development for coastal systems requires consideration of the scale interdependency from individual to global and recognition of the probable global reorganizational emergence of scale-free networks that could cooperate to maximize the integrated sustainability among them.