In the Southern Hemisphere, humpback whales (Megaptera novaeangliae) migrate along the extended continental coastlines of Australia, South America, and South Africa. This study reports on photo-identification capture–recapture data from a long-term survey conducted in Hervey Bay, Queensland, where a substantial proportion of the population stop over early in the southern migration. Photo-identification data were collected over 10 weeks per year from 1997 to 2009. The migration through Hervey Bay is dominated and led by females with high fidelity to the site. Mature females, yearlings, and immature whales use the Bay during August, while mature lactating females with calves dominate during September and October. Complex social behaviours occur throughout the season and differ between the early and late cohorts. We argue that the composition of the two cohorts and their distinctively different behaviours indicate that Hervey Bay is not simply a resting site but an area of aggregation that serves important social and biological benefits. A multistate open robust design model was fitted to capture–recapture data to estimate the annual number of whales visiting the Bay, the permanent emigration rate, proportions of the visiting population that do not enter the Bay each year, the number present during each week, and their residency times. The number of annual visitors to the Bay increased approximately linearly from 857 in 1997 to 2175 at the end of sampling in 2009 with two-thirds migrating through during the first half of each season. The population rate of growth may have been slowing by 2009, but there was considerable uncertainty in the trajectory and little basis for projection into the future. While it is desirable to know the current status of the Hervey Bay population and what has occurred since 2009, the cost and effort required make further manual collection and matching of images unlikely. The development of AI algorithmic matching software may enable further research in future.