Abundance of harbor porpoise (Phocoena phocoena) was estimated from data collected during vessel surveys conducted throughout the inland waters of Southeast Alaska. Line-transect methods were used during 18 seasonal surveys spanning 22 years (1991–2012). Estimates were derived from summer surveys only because of the broader spatial coverage and greater number of surveys during this season than during other seasons. Porpoise abundance varied when different periods were compared (i.e., 1991–1993, 2006–2007, and 2010–2012); however, persistent areas of high porpoise densities occurred in Glacier Bay and Icy Strait, and off the town of Wrangell and Zarembo Island. Overall abundance of harbor porpoise significantly declined from the early 1990s (N=1076, 95% confidence interval [CI]=910–1272) to the mid-2000s (N=604, 95% CI=468–780). This downward trend was followed by a significant increase in the early 2010s (N=975, 95% CI=857–1109) when abundance rose to levels similar to those observed 20 years earlier. Potential factors that could contribute to the downward trend were examined. The 2 regions with high densities of harbor porpoise (i.e., Glacier Bay and Icy Strait as well as Wrangell and Zarembo islands), that were consistently occupied by this species, and the different trend values of these 2 regions indicate that some fine-scale population structuring may exist for harbor porpoise inhabiting the inland waters of Southeast Alaska.