Southern Pacific humpback whales (Megaptera novaeangliae) breed in subtropical and tropical waters off Peru in the south to Nicaragua in the north. The effect of warming oceans on humpback whale distribution in breeding areas remains unclear. We modeled the spatial distribution of humpback whales off the coast of Ecuador in relation to environmental variables. We analyzed the temporal variability in humpback whale sighting rates (animals/hour) in a subtropical (Manabí, 1996–1999) and tropical (Esmeraldas, 2001–2019) breeding ground. At the regional scale, we found humpback whale presence was more likely in shallow waters over the continental shelf. Esmeraldas and Manabí breeding grounds are core wintering habitats with most humpback whale sightings along Ecuador. Within breeding grounds, individual sighting rates varied between and within years and in relation to local sea surface temperature anomalies (SSTa). More animals were sighted in years with cooler waters in the Esmeraldas breeding ground, while the opposite was true in Manabí. Our findings suggest that during ENSO conditions, humpback whales may reach their temperature niche limit in the warm tropical waters near Esmeraldas, while during La Niña conditions, cooler areas such as Peru and Manabi become less suitable, and whales move further north.