The articles in this special feature challenge the presumption that scholars can make simple, predictive models of social-ecological systems (SESs) and deduce universal solutions, panaceas, to problems of overuse or destruction of resources. Moving beyond panaceas to develop cumulative capacities to diagnose the problems and potentialities of linked SESs requires serious study of complex, multivariable, nonlinear, cross-scale, and changing systems. Many variables have been identified by researchers as affecting the patterns of interactions and outcomes observed in empirical studies of SESs. A step toward developing a diagnostic method is taken by organizing these variables in a nested, multitier framework. The framework enables scholars to organize analyses of how attributes of (i) a resource system (e.g., fishery, lake, grazing area), (ii) the resource units generated by that system (e.g., fish, water, fodder), (iii) the users of that system, and (iv) the governance system jointly affect and are indirectly affected by interactions and resulting outcomes achieved at a particular time and place. The framework also enables us to organize how these attributes may affect and be affected by larger socioeconomic, political, and ecological settings in which they are embedded, as well as smaller ones. The framework is intended to be a step toward building a strong interdisciplinary science of complex, multilevel systems that will enable future diagnosticians to match governance arrangements to specific problems embedded in a social-ecological context.