Sea ducks are considered vital indicators of ecosystem health yet are experiencing long-term abundance declines in the transboundary waters of the Salish Sea in Canada and the United States. Identifying the mechanisms driving changes in abundance or causing redistributions within this region necessitates a transboundary effort. Our analysis compiled data from both the British Columbia Coastal Waterbird Survey (BCCWS) and the Puget Sound Seabird Survey (PSSS) between 2009–2022 to assess broad-scale predator-prey interactions between Bald Eagles and priority sea ducks, using a multispecies occupancy model. Our results suggest that Bald Eagles more often than chance overlap with priority sea ducks in the Salish Sea. However, there was no evidence of second-order effects of latitude, longitude, or year on sea duck occurrence in the presence or absence of Bald Eagles, suggesting that these factors are acting independently. Our results not only help resource managers better understand the broad-scale interplay between predators and prey and the co-occurrence probability of priority sea ducks, but this analytical framework and data resource compilation also provide researchers with a foundation from which multi-species interactions and the mechanisms responsible can be disentangled across these transboundary waters.