Payment for ecosystem services (PES) is a market-based policy approach intended to foster land use practices, such as forest conservation or restoration, that protect and improve the benefits from healthy, functioning ecosystems. While PES programs are used globally, they are an especially prominent environmental policy tool in Latin America, where the vast majority are payment for hydrological services (PHS) programs, which incentivize the conservation and restoration of ecosystems associated with water production and clean water for clearly defined water users. As a market mechanism, PHS approaches involve a transactional relationship between upstream and downstream water users who are connected by a shared watershed. While existing literature has highlighted the important role of non-state actors in natural resource management and program effectiveness, few studies have explored the role of stakeholder participation in the context of PHS programs. Building on the collaborative learning approach and the Trinity of Voice framework, we sought to understand how and to what extent PHS program stakeholders are engaged in PHS design, implementation, and evaluation. In this paper we explored (1) the modes of stakeholder engagement in PHS programs that program administrators use, and (2) the degree to which different modes of stakeholder participation allow PHS stakeholders to have decision power with which to influence PHS policy design and expected outcomes. To better understand the role of stakeholder participation, and the different ways participation occurs, we used a comparative multiple-case study analysis of three PHS program administration types (government, non-profit, and a mixed public–private organization) in Mexico and Colombia that have incorporated stakeholder engagement to achieve ecological and social goals. Our analysis draws on institutional interviews to investigate the modes of stakeholder engagement and understand the degree of decision space that is shared with other PHS stakeholders. Across all cases, we found that the trust between key actors and institutions is an essential but underappreciated aspect of successful collaboration within PHS initiatives. We conclude with recommendations for ways in which program administrators and governmental agencies can better understand and facilitate the development of trust in PHS design and implementation, and natural resources management more broadly.