Glacier Bay National Park had one of the largest breeding aggregations of harbor seals in Alaska, and it is functionally the only marine reserve for harbor seals in Alaska; yet, numbers of seals in the Bay are declining rapidly. Understanding why seals in Glacier Bay are declining may clarify their minimal habitat needs. We estimated population trends using models that controlled for environmental and observer-related factors. In 1992, 6,200 seals were counted on icebergs in a tidewater glacial fjord and at terrestrial sites; by 2002 only 2,550 seals were counted at these same haul-outs. Numbers of non-pups in the glacial fjord declined by 6.6%/yr (−39%/8 yr) in June and by 9.6%/yr (−63%/11 yr) in August and at all other haul-outs by 14.5%/yr (−75%/10 yr) during August. In the glacial fjord the number of pups remained steady from 1994 to 1999 and made up an increasing proportion of seals counted (5.4%/yr), and the proportion of pups peaked at 34%–36%. The rapid declines do not appear to be due to changes in seal behavior or redistribution. The declines reinforce genetic evidence that harbor seals in Glacier Bay are demographically isolated from other populations and indicate that current management stocks need to be redefined. Changes in Glacier Bay's ecosystem and population demographic data from the glacial fjord suggest that interspecific competition and predation are likely factors in the declines.