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Complex systems are shaped by cross-scale interactions, nonlinear feedbacks, and uncertainty, among other factors. Transdisciplinary approaches that combine participatory and conventional methods and democratize knowledge to enable diverse inputs, including those from local, informal experts, are essential tools in understanding such systems. The metaphor of a ‘bridge’ to overcome the divide between different disciplines and knowledge systems is often used to advocate for more inclusive approaches. However, there is a shortage of information and consensus on the process, methodologies, and techniques that are appropriate to achieve this. This paper compares two case studies from Peru and South Africa in which community-level assessments were conducted as part of the Millennium Ecosystem Assessment, and explores the different conceptual models used to deal with scale and complexity, the methods adopted to deal with epistemology, and the different means of dealing with uncertainty in each assessment. The paper highlights the conceptual and practical challenges encountered by each assessment and discusses some of the conceptual and practical trade-offs involved in the selection of particular approaches. We argue that a boat navigating between unknown shores may be a more appropriate metaphor than a bridge, whose starting and end points are fixed and known. [ABSTRACT FROM AUTHOR]