In this chapter, we present a proposal for decision aiding in a participatory situation in the real world may constitute, in particular for water management. We first outline the context in which these decision-aiding processes take place: messy inter-organizational settings. We then present some of the available decision-aiding theories and models that could be used and adapt one of these, a decision-aiding process model based on Tsoukiàs (Annals of Operations Research 154:3–27, 2007), for this inter-organizational context. We next highlight how the model was used in a research intervention for the creation of the Lower Hawkesbury Estuary Management Plan in Australia. We demonstrate how this model significantly aided the structuring of the decision-aiding process and promoted insights on its usefulness and validity. We also provide an ex-post operational validation of the Mazri (Apport méthodologique pour la structuration de processus de décision publique en contexte participatif. Le cas des risques industriels majeurs en France, 2007) decision-aiding model for participatory structure design. From the real-world intervention case, we also justify our claims that (1) we need decision-aiding methodologies to improve inter-organizational decision making for water management, as well as theoretical models and problem-structuring methods that can form useful parts of these methodologies; and (2) we need negotiation skills, amongst others, for putting the methodologies in place in the real world. [ABSTRACT FROM AUTHOR]