We conducted standardized surveys for marine birds in Glacier Bay in seven years between 1991 and 2008. From our most recent survey, a combination of line- and strip-transect methods completed in 2008, we estimated that 4981 (95% CI 1293–8670) Kittlitz’s Murrelets Brachyramphus brevirostris resided in Glacier Bay during the month of June, together with 12 195 (5607–18 783) Marbled Murrelets B. marmoratus. When counts were prorated to assign unidentified Brachyramphus murrelets to species, population estimates increased to 5641 Kittlitz’s Murrelets and 13 810 Marbled Murrelets. Our surveys of bird numbers in Glacier Bay between 1991 and 2008 revealed that Kittlitz’s Murrelet declined by ≥85% during this period. Trend analysis suggested a rate of decline between -10.7% and -14.4% per year. No direct human impacts (e.g., bycatch, oil pollution, vessel disturbance) in our study area could fully account for a decline of this magnitude. Widespread declines of Brachyramphus murrelets and Harbor Seals Phoca vitulina in the Gulf of Alaska during the 1980s-1990s suggest large-scale influences on these marine predators, perhaps related to climate-mediated cycles in food supply. Other natural factors that may impact Glacier Bay populations include predation by avian and terrestrial predators, widespread glacial retreat and its effect on nesting and foraging habitats, and competition for food with marine predators whose abundance in Glacier Bay has increased markedly in recent years (Humpback Whales Megaptera novaeangliae and Steller Sea Lions Eumetopias jubatus).