Harbor seals (Phoca vitulina richardii) in the inland waters of Washington were reduced by predator control programs in the twentieth century, but stocks have rebounded since being protected in the 1970s. Three management stocks are recognized, but there is little information on their current abundance. We conducted 38,431 km of aerial line-transect surveys throughout the range of these stocks in 2013-2016, sighting a total of 4,678 groups of harbor seals. Line-transect analysis with Beaufort sea state as a covariate provided estimates of the number of seals in the water. We then incorporated tagging data from 15 instrumented seals to develop correction factors, both for seals missed in the water while diving, and those that were on shore. Tagging data were modeled with generalized linear mixed models to provide estimates of the proportions diving and hauled out. After applying these correction factors, we estimated that the Hood Canal stock contained 1,368 seals (CV = 16.8%), the Southern Puget Sound stock contained 1,976 seals (CV = 20.5%), and the Washington Northern Inland Waters stock contained 7,513 seals (CV = 11.5%). This study presents a non-traditional approach to estimating the size of Washington inland waters harbor seal stocks, which may also be applicable to other species for which survey and tagging data are available.