Understanding habitat use patterns of marine apex predators is of paramount importance for the effective design of conservation plans. Due to their amphibious life cycle, pinnipeds are one of the most vulnerable groups to habitat loss and degradation. Reducing knowledge gaps that still exist regarding temporal changes in tropical pinniped habitat use is therefore of particular importance for conservation efforts. We analyzed terrestrial habitat use phenology of a tropical otariid, the Galapagos sea lion Zalophus wollebaeki. Regular land-based censuses were carried out in Wreck Bay of San Cristóbal Island, Galapagos, between 2008 and 2012 to explore seasonal changes in sea lion abundance, distribution, and preferences among different habitat types. A daily cycle of haul-out patterns was observed. Animals aggregated on sandy beaches during the coldest periods of the day and were more abundant on rocky and artificial structures when air temperature was warmer. The use of artificial floating platforms as resting places by Z. wollebaeki was described for the first time and linked to environmental variability, suggesting that this may be a successful management tool for pinnipeds inhabiting low latitudes. Further, this species demonstrated seasonal distribution changes, aggregating in high densities during warm seasons and maintaining more even distributions during cold seasons. Sea surface temperature, air temperature, and the onset of the breeding season were the variables that most significantly influenced haul-out patterns of Z. wollebaeki, indicating that this species can adapt to changing environmental conditions by displaying a high degree of plasticity regarding its distribution and terrestrial microhabitat preferences.