Recent studies show that human impacts on marine ecosystems are threatening marine biodiversity. A greater emphasis on predicting how predators might respond to changes in the marine environment is needed because the effects of human activities are spatially heterogeneous. Here we analyse rorqual whales distribution data in a highly impacted upwelling region (North-western Iberian coast, Spain). Using a multi-model inference approach this study assesses the habitat drivers of the fine-scale distribution of three endangered whale species (blue, fin and sei whales) as a way to better understand how rorqual whales might respond to human-induced changes in the coastal ecosystem. The unequal use of available habitat, concentrated at the edge of the continental slope (200 m depth and strong bottom slope gradient) in areas with a south-easterly coastal orientation, showed that rorqual whales presented a fine-scale pattern of habitat selection in response to prey availability. Rorqual whales' distribution is affected by the coastal upwelling regime of the Iberian Peninsula, which is known to be under impact of climate change. Therefore, responses of rorqual whales to upwelling changes might be manifested at the population level such as shifts in abundance and distribution. This information contributes to extend the scant information available about the presence of these species in the North-east Atlantic. Our findings provide management agencies with an opportunity to devise and implement adequate adaptation measures which may ameliorate adverse effects critical for the conservation of rorquals in a changing climate.