We conducted land-based counts of harbor seals (Phoca vitulina richardii) and collected related environmental data at Tugidak Island (Gulf of Alaska, 1994–2000) and Nanvak Bay (Bristol Bay, 1990–2000) to estimate population trends and identify factors influencing counts. At Tugidak Island, the seal population declined substantially during molting from 1976 through the 1980s, stabilized in the early 1990s, and increased at a moderate rate (3.4%/yr, CI: 1.0%–5.8%) from 1994 to 2000. Pups and all seals ashore during pupping increased at higher annual rates of 5.4% (CI: 2.2%–8.8%) and 8.3% (CI: 4.5%–12.3%) from 1994 to 2000 at Tugidak Island. At Nanvak Bay seals declined in abundance between 1975 and 1990 but increased during the 1990s at 9.2%/yr (CI: 7.2%–11.3%) during pupping and 2.1%/yr (CI: 0.6%–3.6%) during molting. Date and time-of-day were significant covariates in all analyses. Factors that led to declines at Tugidak Island and Nanvak Bay have seemingly abated sufficiently such that these populations are currently increasing, though still greatly reduced from the 1970s. Index sites are useful adjuncts to aerial surveys, providing survey-related information not always available from aerial counts, which is useful in survey design and data analysis.