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Background: Extralimital observations of pinnipeds are important to understand the effects of changing climates on our oceans and the distribution of these species. The southern elephant seal (Mirounga leonina) is a known vagrant species that moves over long distances. We report three new records of M. leonina in interior freshwater tributaries of the Guayas River Estuary Basin (Gulf of Guayaquil) and northern coast of Ecuador between October 2017 and January 2018 during a cold episode of La Nina event in the southeastern Pacific. Results: The elephant seals were identified according to their large size (~ 5 m for adult and 2–3 m for juveniles/subadults), the head to neck size ratio, and the size and external morphology of the proboscis, which was used as a key trait to differentiate M. leonina from the Northern elephant seal (M. angustirostris). The observations of M. leonina in Ecuador highlight an extreme movement covering an assumed total distance of approximately 8000 km from the circumpolar region. The cold event "La Niña" with sea surface temperature anomalies ranging − 1.5 °C to − 0.5 °C in October 2017 likely triggered the extralimital movements of these animals. Conclusion: Recurring observations of M. leonina in the Guayaquil Gulf suggest the importance of this highly productive region and tropical estuarine-riverine habitats as temporary haulout sites for resting. These new findings indicate that vagrant individuals influenced by oceanographic events and eco-physiological processes are reaching this region more frequently than previously thought. [ABSTRACT FROM AUTHOR]