Human activities contribute to the degradation of water quality on the Galapagos Islands, affecting human health and Galapagos’ fragile ecosystem. Despite the numerous resources vested in water management, programs have yet to achieve measurable improvements in water quality. To identify the governance mechanisms and barriers to improving water quality, we applied a two-pronged strategy: a collaborative, bottom-up compilation and prioritization of technical specialists and stakeholders’ concerns, and an evaluation of top-down government plans. The comparison of priorities and programs shows four major themes that require attention: barriers to better governance, community involvement, research, and policy. The islands lack a transparent method for accountability of the funds designated for water management, the efficacy of implementation, and results and progress beyond government periods. Government projects have included limited public participation, resulting in projects that do not meet stakeholder’s needs and concerns. Furthermore, the majority of the programs have not been completed within the timeline or budgets allocated. We recommend implementing a participatory governance mechanism that responds to each island’s context, balances socioecological and policy priorities and evaluates past projects to have adequate benchmarking, mitigating a planning fallacy. All programs should be accompanied by a transparent monitoring system that ensures accountability and evaluates water quality programs’ efficiency and effectiveness, according to goals and indicators developed collaboratively. This research may aid practitioners in small island developing states (SIDS) around the globe that are struggling with similar water management and governance issues and who may benefit from taking a bottom-up and top-down approach to assessing technical specialists’ and local stakeholders’ concerns in relation to past, present and future government programs.