Studies on population abundance variations at different temporal scales contribute to the understanding on how these populations change over time and what are the factors influencing those variations. We analyzed daily, monthly and annual haul-out abundance patterns of South American sea lions (SASL, Otaria flavescens) in 2 breeding colonies of the north of Chile. Additionally we analyzed the effect of El Nino events on the sea lions' annual patterns. The abundance of sea lions in Punta Negra (PN) decreased from 1994 to 2011, whereas in Punta Patache (PP) increased, although the number of pups was proportionately low. Our results indicated a strong effect of El Nino over the abundance of sea lions, especially for females + juveniles in PN. The haul-out monthly abundance of females and juveniles increased during austral winter months, whereas adult and subadult males did not show a clear pattern. Finally, the haul-out abundance tended to increase throughout the day reaching a maximum by late afternoon, especially for females and juveniles. No difference in daily patterns between breeding and non-breeding seasons for any of the sex/age classes was found. This study shows that the number of animals in the PP and PN breeding colonies presented annual, monthly and daily periodicities, and that these periodicities are conditioned by both intrinsic (e.g., breeding period) and extrinsic (e.g., time of day, El Nino) factors. On an annual basis, our results indicate that even at a local scale, SASL population trends at 2 colonies may be different.