The movement of waterfowl across the Pacific Flyway creates ecological interdependencies across the entire landscape. However, management of waterfowl is fragmented between organizations operating at various scales, in different sectors, and within multiple jurisdictions creating a need for cross-boundary collaboration. We aim to evaluate drivers of collaboration nested within regional Migratory Bird Joint Venture partnerships. Based on 221 survey responses (34% response rate), we created a governance network of 1,153 organizations. We analyzed the waterfowl management network using valued exponential random graph models based on types of collaborative activities in which organizations engage. Results show that collaboration is particularly driven by state agencies and organizations operating at a regional scale. Involvement in Joint Ventures significantly increases the likelihood that any organization will collaborate in the broader management network. There are also significant differences between collaboration within each Joint Venture region. Organizations working within the Central Valley and California Central Coast regions are significantly more likely to engage in collaboration. These patterns reflect both ecological patterns of waterfowl as well as institutional dynamics of regional management structures. This work reveals a more complex picture of social-ecological alignment, necessitating future research of nuanced ecological patterns and regional differences in management.