Natural selection should favour strategies that maximise reproductive success. Females may use different resources during progressive stages of reproduction according to energetic demands, behavioural constraints and prey availability. We used South American fur seal, Arctocephalus australis australis, pup whisker isotope values as proxies for maternal diet and habitat use to determine how resource use (1) changes throughout pup development from in utero growth to mid-end of lactation and (2) how it differs among individuals. The longest whisker was cut from 5 male and 5 female fur seal pups (of approximately 8 months of age) at Bird Island, Falkland Islands, in 2018, and δ15N values and δ13C values were analysed every 5 mm along the length of each whisker. Patterns in δ13C values indicated that mothers used different habitats during the annual cycle, likely coinciding with seasonal shifts in prey availability or distribution. The individual specialisation index based on δ13C values was 0.34, indicating that adult females used different habitats, which could reduce intra-specific competition and ultimately enhance pup growth and survival. An increase in δ15N values occurred along every pup whisker from pup birth to mid-end of lactation, which likely reflected trophic enrichment related to suckling and fasting by pups, overriding the maternal isotopic signature. Pup whisker stable isotopes are useful proxies of maternal foraging ecology. However, physiological processes complicate interpretations by altering δ15N values. Interpreting these values therefore requires additional knowledge of the species’ ecology and physiology.