Many migratory species are in decline and understanding these declines is challenging because individuals occupy widely divergent and geographically distant habitats during a single year and therefore populations across the range are interconnected in complex ways. Network modeling has been used to show, theoretically, that shifts in migratory connectivity patterns can occur in response to habitat or climate changes and that habitat loss in one region can affect sub-populations in regions that are not directly connected. Here, we use a network model, parameterized by integrating long-term monitoring data with direct tracking of -100 individuals, to explain population trends in the rapidly declining Wood Thrush (Hylocichla mustelina) and to predict future trends. Our model suggests that species-level declines in Wood Thrush are driven primarily by tropical deforestation in Central America but that protection of breeding habitat in some regions is necessary to prevent shifts in migratory connectivity and to sustain populations in all breeding regions. The model illustrates how shifts in migratory connectivity may lead to unexpected population declines in key regions. We highlight current knowledge gaps that make modeling full life-cycle population demographics in migratory species challenging but also demonstrate that modeling can inform conservation while these gaps are being filled.