This chapter presents the fundamentals of participatory system dynamics modelling (PSDM) and a set of applications in ecological economics. It provides an overview of case studies to derive a set of lessons from practice in six different projects covering six distinct topics: maritime policies, sustainable food consumption, degrowth, river basin governance, coastal zone management, and protected areas management. PSDM has developed as a promising method to facilitate the engagement of stakeholders in environmental and sustainability decision processes. It offers a platform for structured deliberation, involving stakeholder groups in problem conceptualisation, policy formulation and assessment. System dynamics has been used for a long time in ecological economics, providing a synthesis framework in problem-solving processes and powerful tools for scenario based analysis. The two main tools for building system dynamics models are Causal Loop Diagrams (CLDs) and Stock-and-Flow Diagrams (SFDs). A generic participatory modelling project typically develops in three stages, such as, preparation, workshops, and follow-up and evaluation.