The largest aggregations of harbor seals (Phoca vitulina) in Alaska, USA, haul out on floating ice in tidewater glacial fjords. Seals use these fjords in peak numbers during the critical periods of pupping, breeding, and molting when visits by tour ships also peak. Documented and suspected declines of harbor seals in fjords with rising vessel traffic underscore the need to better understand possible impacts, particularly in areas where ship visits have risen substantially in the past 2 decades. We examined the interruption of haul-out bouts of harbor seals due to approaching cruise ships in Disenchantment Bay, Alaska. We conducted observations from cruise ships and focused on disturbance of seals as evidenced by seals flushing into the water from the floating ice on which they rested. We investigated rate of flushing in relation to vessel distance, approach angle, group size, and seal type (mother, pup, or other). Using a survival-regression analysis, we found that the risk of disturbing harbor seals increased when ships approached within 500 m; seals approached as close as 100 m were 25 times more likely to enter the water than seals 500 m from a ship. Seals were 4 times more prone to enter the water when ships were approaching directly rather than passing abeam. Seals responded similarly regardless of group size or seal type. Energetic models indicated a potential to disrupt energy balance and cause thermal stress in disturbed pups if they spent >50% of their time in ice-chilled water. Studies at non-glacial sites suggest that pups spend 40–70% of their time in the water. Voluntary guidelines for approaching seals in Alaska recommend that cruise ships approach ≥91 m (100 yards), a distance at which we show 90% of seals would flush into the water. Our findings indicate a need to develop regulations to maintain a 500-m separation between cruise ships and seals in all Alaskan glacial fjords.