Climate change influences apex predators in complex ways, due to their important trophic position, capacity for resource plasticity, and sensitivity to numerous anthropogenic stressors. Bald eagles, an ecologically and culturally significant apex predator, congregate seasonally in high densities on salmon spawning rivers across the Pacific Northwest. One of the largest eagle concentrations is in the Skagit River watershed, which connects the montane wilderness of North Cascades National Park to the Puget Sound. Using multiple long-term datasets, we evaluated the relationship between local bald eagle abundance, chum and coho salmon availability and phenology, and the number and timing of flood events in the Skagit River. We analyzed both changes over time as a reflection of climate change impacts, as well as differences between managed and unmanaged portions of the river. We found that peaks in chum salmon and bald eagle presence have advanced at remarkably similar rates (~0.45 days/year), suggesting synchronous phenological responses within this trophic relationship.Yet the temporal relationship between chum salmon spawning and flood events, which remove salmon carcasses from the system, has not remained constant. This has resulted in a paradigm shift whereby the peak of chum spawning now occurs before the first flood event of the season rather than after. The interval between peak chum and first flood event was a significant predictor of bald eagle presence: as this interval grew over time (by nearly a day per year), bald eagle counts declined, with a steady decrease in bald eagle observations since 2002. River section was also an important factor, with fewer flood events and more eagle observations occurring in the river section experiencing direct hydroelectric flow management.