Understanding the population dynamics of marine mammals is essential for assessing their resilience to historical harvesting pressures and current anthropogenic threats. The South American sea lion (SASL, Otaria byronia), widely distributed along the South American coasts, represents the largest biomass of northern and central Patagonia. This species faces threats such as incidental fishing captures, aquaculture, and tourism, with well-documented impacts on its population. However, the effects of Highly Pathogenic Avian Influenza (HPAI) H5N1 on its population dynamics are poorly understood. This study provides new insights into the impact of the 2023 avian influenza outbreak on the SASL in northern Patagonia. Population trends and age-sex class composition of colonies were updated, incorporating the HPAI outbreak in the Río Negro rookeries to compare trends before and after the epizootic event. A positive trend in SASL abundance was observed from 2007 to 2022 across most age and sex classes. However, in the 2024 census, 7175?±?145 individuals were counted across three colonies, with the largest, Punta Bermeja, recording a 27.6% decline. During the 2023 outbreak, 1476 deaths were reported, affecting all age and sex classes. These findings suggest the HPAI H5N1 outbreak significantly impacted the previously positive population trend.