Summer breeding populations of Kittlitz's Murrelets (Brachyramphus brevirostris) have declined by 80–90% in southeastern Alaska during the past 25 years. Boating activities overlap considerably in space and time with Kittlitz's Murrelets in Glacier Bay, and disturbance could affect individuals by causing them to fly away from preferred foraging sites, thereby disrupting foraging bouts or resting periods. We observed the effects of vessel activity on Kittlitz's Murrelets at sea for each of three response variables (density, group size, and behaviors) in Glacier Bay. Response variables were characterized at three time-scales of inference: immediate (instantaneous response to vessel passage), short-term (response that persisted 30 min after vessel passage), and daily (response on days with different vessel traffic rates). Group size was not affected by vessel activity. By contrast, near-shore densities were suppressed temporarily by vessel passage but recovered within the day. Density effects did not persist at the daily time-scale and, therefore, did not result in persistent loss of foraging habitat for Kittlitz's Murrelets. Also, behavior was affected at both the immediate and daily time-scales, but not at the short-term time-scale, and may have affected Kittlitz's Murrelets by increasing the amount of time spent flying, which is energetically costly. Vessel passage caused a 30-fold increase in flight behavior (from 0% to 30%). Large and fast-moving vessels caused the greatest disturbance to Kittlitz's Murrelets, which has implications for management of vessel activity.