Understanding causation in social-ecological systems (SES) is indispensable for promoting sustainable outcomes. However, the study of such causal relations is challenging because they are often complex and intertwined, and their analysis involves diverse disciplines. Although there is agreement that no single research approach (RA) can comprehensively explain SES phenomena, there is a lack of ability to deal with this diversity. Underlying this diversity and the challenge of dealing with it are different causal reasonings that are rarely explicit. Awareness of hidden assumptions is essential for understanding how the causal reasoning of an RA is constituted, and for promoting the integration, translation, or juxtaposition of different RAs. We identify the following elements as particularly relevant for understanding causal reasoning: methods, frameworks and theories, accounts of causation, analytical focus, and causal notions. We begin with the idea that one of these elements typically figures as an entry point to an RA. This entry point is particularly important because it generates a path dependence that orients causal reasoning. In a subsequent step, when an approach is applied, causal reasoning concretizes as a result of a particular constellation of the remaining elements. We come to these insights by studying the application of four different RAs to the same social-ecological case (the collapse of Baltic cod stocks in the 1980s). On the basis of our findings we developed a guide for the analysis of causal reasoning by raising awareness of the assumptions, key elements, and the relations between these key elements for a given RA. The guide can be used to elicit the causal reasoning of RAs, facilitate interdisciplinary collaboration, and support disclosure of ethical/political dimensions that underlie management/governance interventions that are formulated on the basis of causal findings of research studies.