Scientists and policymakers increasingly recognize the critical dependence of urban and agricultural economies and livelihoods on mountain systems. Mountain systems feed critical watersheds, provide diverse commodities, enable recreation, and host competing settlement uses that also affect downstream water quality and quantity in aquifers, lakes, and streams. Many scientists from diverse disciplines are focused on the problem of how to govern common water systems that are subject to diverse—often competing—property regimes, organizational/agency interests, and national, local, state, and indigenous jurisdictions. Given the political obstacles to creation of nested organizational authorities, the current literature suggests that organizational actors may collaborate based on water's shared importance and build voluntary systems of networked governance that produce beneficial institutional relations and political regimes. Barriers to this ideal of collaboration include competing legal rights, identity politics, and state or national boundaries at larger scales. A key question arises: How can staff of relevant agencies, who are concerned about the threats to environmental goods, work toward cooperative governance when certain barriers impede collaboration between their organizations? We explore this question based on the case example of a complex aquifer and related river system in northern Idaho and eastern Washington that are transected by competing state, tribal, and local jurisdictions and are impacted by historic mining pollution, deforestation, and recent amenity-driven urbanization. Exploratory interviews with agency actors, document analysis, and observation of collaborative meetings confirm that individual employees can be key actors in developing transboundary governance, despite legal and organizational impediments to collaboration between their organizations. The case supports recent literature on scalar politics that shifts the emphasis away from ideal structures and focuses instead on better understanding of the ways in which creative actors may build collaborative institutions within existing structures.