Estimating total number of birds using a particular staging site during migration is challenging because counts alone do not account for turnover in the local population. Robust statistical methods are needed to more fully assess the conservation value of such sites. We used the multi-strata model in Program MARK to estimate time-dependent transition probabilities between sequential staging sites to estimate lengths of stay for spring-staging Pacific black brant (Branta bernicla nigricans) on the Fraser River delta and Parksville-Qualicum areas in the Strait of Georgia, British Columbia, Canada. Using resightings of marked individuals in combination with ground counts, we estimated the total number of brant, with associated uncertainties, staging at these sites during the spring migrations of 1999 and 2000. We estimated between 28,927 and 33,181 individual brant transited the Fraser River delta and Parksville-Qualicum sites in 1999 and between 21,621 and 25,405 individuals in 2000. These totals correspond to approximately 18–26% of the entire Pacific Flyway brant population, suggesting the need for continued conservation and management efforts at these sites. Given the importance of staging sites to migratory populations, we believe this method could be applied to other species and locations.