Monitoring health and stress in free-ranging populations is an important aspect of conservation management. Seal Rocks, Victoria, is the largest Australian fur seal (Arctocephalus pusillus doriferus) breeding colony, but has one of the highest rates of decline in live pup abundance for the species, and the shortest vessel approach distances. Pups from the 2021 and 2022 breeding seasons were sampled at 3-6 weeks of age (peak vessel visitation, n=180) and 5-6 months of age (off-peak vessel visitation, n=172). Haematological and morphometric parameters, neutrophil:lymphocyte (N:L) ratios, and stress hormone concentrations in pup fur were used to evaluate health and stress. Haematological and morphometric parameters differed significantly (P<0.05) between peak and off-peak seasons. Stress hormones and N:L ratios were significantly higher in peak compared to off-peak seasons, indicating higher exposure to stress during foetal and neonatal development, respectively, compared to when pups were older. The differences in pup health and stress parameters between peak and off-peak vessel visitation highlight the increased vulnerability of pups when the potential for human disturbance is highest. Results support the need for enhanced protection from anthropogenic stressors during a period of critical development and provide a point of comparison for future monitoring.