Conservation planning for large ecosystems has multiple benefits but is often challenging to implement because of the multiple jurisdictions, species, and habitats involved. In addition, decision making at large spatial scales can be hampered because many approaches do not explicitly incorporate potentially competing values and concerns of stakeholders. After the Deepwater Horizon oil spill, establishing baselines was challenging because of (1) variation in study designs, (2) inconsistent use of explicit objectives and hypotheses, (3) inconsistent use of standardized monitoring protocols, and (4) variation in spatial and temporal scope associated with avian monitoring projects before the spill. Herein, we show how the Gulf of Mexico Avian Monitoring Network members used structured decision making to identify bird monitoring priorities. We used multiple tools and techniques to clearly define the problem and stakeholder objectives and to identify bird monitoring priorities at the scale of the entire northern Gulf of Mexico region. Although our example is specific to the northern Gulf of Mexico, this approach provides an example of how stakeholder values can be incorporated into the coordination process of broad-scale monitoring programs to address management, restoration, and scientific questions in other ecosystems and for other taxa.