There is increasing concern over anthropogenic pressures on species and ecosystems, particularly as their cumulative impacts remain difficult to measure and predict. Pygmy blue whales (Balaenoptera musculus brevicauda), whose populations remain a fraction of their historical size due to historical whaling, are highly vulnerable to anthropogenic threats. As a migratory species, they are exposed to a range of impacts both in localised areas and along their migratory routes. Geographe Bay, southwestern Australia, has been identified as an important migratory area for the southeast Indian Ocean (SEIO) population of pygmy blue whales during their southern migration. Using a 30-year dataset (1994–2024) from a combination of systematic and haphazard vessel surveys, we estimated the abundance and distribution of the proportion of the SEIO pygmy blue whale population migrating through this region. While annual abundance varies, their distribution remains relatively consistent, overlapping with both Commonwealth and State Marine Parks. Furthermore, pygmy blue whales often travel in proximity to the declared Offshore Wind Farm Area near Bunbury, where cumulative human pressures may increase. These results provide critical information for managers, particularly for developing strategies that can mitigate cumulative threats and provide protection for this endangered species.