While population sizes and structures naturally fluctuate over time, rapid within-generation changes are usually driven by shifts in habitat quality and (or) abrupt mortality. We evaluate how sperm whales (Physeter macrocephalus L., 1758 = Physeter catodon L., 1758) responded to the dynamic habit off the Galápagos Islands over 30 years, relating it to variation in prey availability and whaling operations in the tropical Pacific. In the 1980s, males and females were commonly sighted foraging and socializing in the northwest of the archipelago. Sightings decreased during the 1990s; by the 2000s, they became very rare: occasional single foraging males were sighted and females abandoned the archipelago. In the 2010s, whales return to the southern waters, in large groups with apparently more breeding males and calves. The waxing and waning of Galápagos sperm whales are likely caused by environmental shifts together with ripple effects of whaling. Their patchy prey are influenced by variation in sea temperature and productivity, which drives movements of whales in and out of the archipelago. Whaling may have aggravated these movements by leaving an attractive surplus of prey in coastal waters depleted of whales. These findings highlight the magnitude of spatiotemporal scales used by sperm whales and the consequent challenges of assessing population dynamics of long-lived, mobile pelagic species.