ABSTRACT: Blue whales Balaenoptera musculus aggregate to feed in a regional upwelling system during November–May between the Great Australian Bight (GAB) and Bass Strait. We analysed sightings from aerial surveys over 6 upwelling seasons (2001–02 to 2006–07) to assess within-season patterns of blue whale habitat selection, distribution, and relative abundance. Habitat variables were modelled using a general linear model (GLM) that ranked sea surface temperature (SST) and sea surface chlorophyll (SSC) of equal importance, followed by depth, distance to shore, SSC gradient, distance to shelf break, and SST gradient. Further discrimination by hierarchical partitioning indicated that SST accounted for 84.4% of variation in blue whale presence explained by the model, and that probability of sightings increased with increasing SST. The large study area was resolved into 3 zones showing diversity of habitat from the shallow narrow shelf and associated surface upwelling of the central zone, to the relatively deep upper slope waters, broad shelf and variable upwelling of the western zone, and the intermediate features of the eastern zone. Density kernel estimation showed a trend in distribution from the west during November–December, spreading south-eastward along the shelf throughout the central and eastern zones during January–April, with the central zone most consistently utilised. Encounter rates in central and eastern zones peaked in February, coinciding with peak upwelling intensity and primary productivity. Blue whales avoided inshore upwelling centres, selecting SST ~1°C cooler than remotely sensed ambient SST. Whales selected significantly higher SSC in the central and eastern zones than the western zone, where relative abundance was extremely variable. Most animals departed from the feeding ground by late April.