Emerging infectious diseases can cause abrupt demographic changes in wildlife populations. The 2023 outbreak of highly pathogenic avian influenza caused widespread mortality in pinnipeds along the South American coast. We evaluated the population-level impact of the outbreak on South American sea lions (Otaria flavescens) and South American fur seals (Arctocephalus australis) in Patagonia, Argentina. Censuses conducted during the 2024 breeding season using aircraft and drones were compared with long-term pre-outbreak data (1973-2023) using two complementary approaches: raw census comparisons and colony trend projections. Raw census comparisons indicated proportional declines in counts of 17.07% in South American sea lions and 31.31% in South American fur seals between the most recent pre-outbreak censuses and the 2024 breeding season. Colony trend projections based on historical growth trajectories suggested outbreak-associated mortality of about 43.67% in South American sea lions and 15.01% in South American fur seals. Adult males exhibited the largest proportional declines in counts in both species. Pup production in 2024 was 54.17% lower than expected in South American sea lions and 45.01% lower in South American fur seals relative to projected values based on pre-outbreak colony trends. Differences in colony density, spatial distribution, and seasonal timing of breeding and haul-out likely contributed to the observed interspecific variability in mortality and reproductive output. The magnitude of adult losses and reduced pup production suggests that the outbreak may influence short- to medium-term population trajectories. Our results highlight the value of long-term census programs for detecting large-scale demographic impacts of emerging infectious diseases in recovering pinniped populations.