Otoliths preserve a continuous geochemical record of its life history, from the earliest natal stage through to adulthood. Using in situ laser ablation (UV) multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) measurements of Sr isotopic compositions together with elemental abundances (Ca, Sr, Ba and Mg), we show how it is possible to characterise the various types of habitats encountered throughout the lifecycle history of individual barramundi. Unlike trace element concentrations, which can be modulated by physiological processes, Sr isotopic compositions of otoliths provide a direct fingerprint of the water mass in which the fish lived. Elemental abundances, in particular Sr/Ba ratios are, however, shown to be especially sensitive to transitional environments, such as estuaries. The flexibility of the barramundi’s life history is confirmed by the present study, with the existence of both marine and freshwater nurseries, with some individuals spending their entire life cycle in fresh water, some entirely in marine and others moving between freshwater estuarine and marine habitats.