From the Habitat Directive to the recent Marine Strategy Framework Directive, the conservation status of cetaceans in European water has been of concern for over two decades. In this study, a seasonal comparison of the abundance and distribution of cetaceans was carried out in two contrasted regions of the Eastern North Atlantic, the Bay of Biscay and the English Channel. Estimates were obtained in the two sub-regions (375,000 km²) from large aerial surveys conducted in the winter (November 2011 to February 2012) and in the summer (May to August 2012). The most abundant species encountered in the Channel, the harbour porpoise, displayed strong seasonal variations in its distribution but a stable abundance (18,000 individuals, CV=30%). In the Bay of Biscay, abundance and distribution patterns of common / striped dolphins varied from 285,000 individuals (95% CI: 174,000–481,000) in the winter, preferentially distributed close to the shelf break, to 494,000 individuals (95% CI: 342,000 − 719,000) distributed beyond the shelf break in summer. Baleen whales also exhibited an increase of their density in summer. Sseasonal abundances of bottlenose dolphins were quite stable, with a large number of ‘pelagic’ encounters offshore in winter. No significant seasonal difference was estimated for pilot whales and sperm whale. These surveys provided baseline estimates to inform policies to be developed, or for existing conservation instruments such as the Habitats Directive. In addition, our results supported the hypothesis of a shift in the summer distributions of some species such as harbour porpoise and minke whale in European waters