The pygmy hippopotamus (Choeropsis liberiensis, Morton, 1849) is classified as Endangered by the International Union for the Conservation of Nature (IUCN). Compared to other large, threatened mammals, this species remains relatively understudied and new findings indicate potential welfare concerns, emphasizing the need for further research on the species welfare in zoological institutions. One approach to improving welfare in captivity is through environmental enrichment. This study investigated the effects of olfactory enrichment on three individual pygmy hippopotamuses through behavioral analysis and heat-map visualization. Using continuous focal sampling, several behaviors were influenced by the stimuli, with results showing a general decrease in inactivity and an increase in environmental engagement and interaction, particularly through scenting behavior. To further enhance behavioral quantification, machine learning techniques were applied to video data, comparing manual and automated behavior classification using the pose estimation program SLEAP. Four behaviors Standing, Locomotion, Feeding/Foraging, and Lying Down were compared. A confusion matrix, time budgets, and Kendall’s Coefficient of Concordance (W) were used to assess agreement between methods. The results showed a strong and moderate agreement between manual and automated annotations, for the female and calf, respectively. This demonstrates the potential of automation to complement behavioral observations in future welfare monitoring.