The impacts of outside interventions on community-based natural resource management are inherently complex, particularly in dynamic political and environmental contexts. As development projects are increasingly participatory, the relationships between stakeholders have become as critical as the innovations themselves. Demands on safe water supplies among the most resourcestressed populations in West Africa are challenging development practitioners to reevaluate their partnerships to retain focus on community need, rather than on operational imperatives. Fieldwork was conducted between 2006 and 2009 using complementary mixed methods to evaluate a range of structural and behavioral mechanisms shaping water management among farming households in south-central Mali. Examining institutional support, in terms of policy and programming, along with the experiences and perceptions of water users, traditional village leadership, nongovernmental organization (NGO) staff, and government representatives, highlighted many challenges that limit sustainable collaborative development. A gendered-approach to data collection was used to delineate barriers and opportunities for decision-making by marginalized water users. The key challenges that limit the success of development efforts in improving water resource management are 1) the legitimacy of community-based organizations that lack traditional authority as perceived by members of households, 2) poor perceptions of resource-strapped decentralized government agencies by rural communities, and 3) superficial participation of marginalized populations in local decision-making. In the majority of the study villages, these challenges have led to the decline of institutional and physical infrastructure intended to improve local water resource management. Opportunities do exist, however, to engage men and women differently in development interventions to increase participation, promote inclusion, and generate lasting partnerships among rural communities, NGOs, and government agencies. These opportunities require compromises to balance the legitimacy of traditional authority with outside development agendas. It is especially important for NGOs, whose roles in local resource management and civil society often fill a necessary void left by government, to capture these opportunities. Keywords: Community-based resource management, water, collaboration, gender, participation, community-based organization, decentralization, government, NGOs