Infectious disease threatens biodiversity and human health on a global scale, and disease emergence may become more common as humans further encroach on habitats and modify environments. To accurately assess the risk of disease emergence in free-ranging populations of vertebrates, we require an understanding of the dynamics of immunity in the wild. We applied techniques from the emergent discipline of ecological immunology to describe immune activity and dynamics in the endangered Galapagos sea lion Zalophus wollebaeki, which is threatened simultaneously by disease from domestic animals and fluctuations in food supply driven by unpredictable environmental variation. We compared immune activity from shortly after birth until 2 years of age between two Galapagos sea lion colonies: one heavily influenced by humans and the other on an uninhabited island, using a generalized linear model framework. Controlling for development, immune activity was higher in the human-impacted colony, as assessed with both humoural and cellular immune components and cumulative and snapshot measures of immune activity. We discuss the possibility that sea lions in the human-impacted colony are under greater immunostimulatory pressure than those in the comparison colony, which could have implications for individual fitness, colony stability and the risk of disease emergence. The study demonstrates the utility of a generalized and widely applicable approach to quantifying immune activity in wild vertebrates, as it highlights important aspects of the system for targeted analysis and further study.