Tidewater glacial fjords support the largest populations of harbor seals (Phoca vitulina richardii) in Alaska and are a prime destination for tour ships. Chronic disturbance from ships, however subtle, could impact long-term population stability. We examined variation in abundance and distribution of harbor seals on floating ice in Disenchantment Bay, Alaska, a tour ship destination for over a century with near daily visitation by ships in the spring/summer over the last decade. Counts of seals by aerial transect showed a sharp decline in May, prior to pupping and the first ships arriving; counts rebounded by the end of June remaining high until August. Seal distribution and abundance peaked in 5–7 tenths ice cover; total area of ice cover showed no effect. Despite regular flushing of seals by ships, we found no broad-scale patterns in seal abundance and distribution that could be explained by ship presence. We cannot rule out mechanisms of long-term disturbance, difficult to detect and that might explain notable differences with other, similar sites. Population declines at disturbed glacial sites and the still rising popularity of vessel-based tourism indicate a need for individual-based studies on how seals respond to the dynamics of glacial ice environments and human-caused stresses.