Complexity science and systems thinking are increasingly recognized as relevant paradigms for studying systems where biology, psychology, and socioenvironmental factors interact. The application of systems thinking, however, often stops at developing a conceptual model that visualizes the mapping of causal links within a system, e.g., a causal loop diagram (CLD). While this is an important contribution in itself, it is imperative to subsequently formulate a computable version of a CLD in order to interpret the dynamics of the modeled system and simulate “what if” scenarios. We propose to realize this by deriving knowledge from experts’ mental models in biopsychosocial domains. This article first describes the steps required for capturing expert knowledge in a CLD such that it may result in a computational system dynamics model (SDM). For this purpose, we introduce several annotations to the CLD that facilitate this intended conversion. This annotated CLD (aCLD) includes sources of evidence, intermediary variables, functional forms of causal links, and the distinction between uncertain and known-to-be-absent causal links. We propose an algorithm for developing an aCLD that includes these annotations. We then describe how to formulate an SDM based on the aCLD. The described steps for this conversion help identify, quantify, and potentially reduce sources of uncertainty and obtain confidence in the results of the SDM’s simulations. We utilize a running example that illustrates each step of this conversion process. The systematic approach described in this article facilitates and advances the application of computational science methods to biopsychosocial systems.