Substantive stakeholder engagement is increasingly recognized as essential for effective water resource development. Infrastructure development projects and strategies are however typically designed by engineers first before initiating discussions about impacts with stakeholders. In altering this sequence, designing meaningful participatory planning processes needs careful attention. This requires an innovative approach taking into account the institutional and discursive structure of the negotiation arena. This study uses eight features of participation and related micro-politics questions to scrutinize the design process of two water resource development projects in Thailand. The research shows that in one case some of the affected stakeholders were excluded, and in the other case, a lack of trust made one village obstruct the design process from the start. In both cases, the capacity to facilitate the negotiation about alternative designs and compensation was deficient. It is concluded that participation should be institutionalized and facilitated in a way that fosters accountable representation by all stakeholders, builds trust, and recognizes stakeholder interests and knowledge. The approach taken helps to understand the outcomes of the planning process and is useful to design planning processes that foster the accountable representation of all stakeholders and the recognition of their interests and knowledge.