Conservation of long-distance migratory species poses unique challenges. Migratory connectivity—that is, the extent to which groupings of individuals at breeding sites are maintained in wintering areas—is frequently used to evaluate population structure and assess use of key habitat areas. However, for species with complex or variable annual-cycle movements, this traditional bimodal framework of migratory connectivity may be overly simplistic. Like many other waterfowl, sea ducks often travel to specific pre- and post-breeding sites outside their nesting and wintering areas to prepare for migration and, in some cases, molt their flight feathers. These additional molt migrations may play a key role in population structure, but are not included in traditional models of migratory connectivity. Network analysis, which applies graph theory to assess landscape connectivity, offers a powerful tool for quantitatively assessing the contributions of different sites used throughout the annual cycle to complex spatial networks. We collected satellite telemetry data on annual cycle movements of over 500 individual sea ducks of five species from throughout eastern North America and the Great Lakes. From these data, we constructed a multi-species network model of migratory patterns and site use over the course of the breeding, molting, wintering, and migration periods. Our results highlight inter- and intra-specific differences in the patterns and complexity of annual-cycle movement patterns, including the central importance of staging and molting sites in James Bay and the St. Lawrence River to multi-species habitat connectivity. We also discuss potential applications of network migration models to conservation prioritization, identification of population units, and integrating different data streams.