Understanding the relationships between cetaceans and their environment is crucial for conservation. This study examined humpback whales in Bahía de Banderas, Mexico, identifying key calving habitats. From 2018 to 2023, 1066 sightings were recorded, including 242 mother–calf groups, 109 mating groups, and 715 other groups. Spatial analysis revealed a non-random distribution; both the Kruskal–Wallis and Wilcoxon–Mann–Whitney tests detected significant differences (P < 0.05) in site preferences. Calving mothers favoured habitats with a mean depth of 59 m and a distance of 2 km from the coast, while mating groups preferred locations at 126 m and 4 km, and other groups chose areas at 149 m and 4 km. All groups were found in relatively flat areas around 2° seafloor slope. A dispersion test indicated a significant relationship between the location of calving mothers and environmental factors. K-means clustering showed 83.6% of calving mothers' sightings at depths less than 40 m and 2 km from the coast. Ensemble species distribution models identified three critical calving areas: one large area (261.8 km2) along the north coast and two smaller areas (9.5 and 5.4 km2) at the southern end of the bay. This study highlights Bahía de Banderas as a vital breeding habitat for humpback whales, providing insights for conservation strategies to protect calving grounds during the breeding season.