Stable isotope analyses, particularly of carbon (δ13C) and nitrogen (δ15N), are used to investigate ecological relationships among species. For marine predators, research has shown the main factors influencing their intra-specific and intra-individual isotopic variation are geographical movements and changes in the composition of diet over time. However, as the differences seen may be the result of changes in the prey items consumed, a change in feeding location or the combination of both, knowledge of the temporal and spatial consistency in the isotopic values of prey becomes crucial for making accurate inferences about predator diets. This study used an abundant marine predator, the Australasian gannet (Morus serrator), as prey sampler to investigate the annual variation in fish and squid prey isotope values over a four-year period (2012-2015) and the geographic variation between two sites with contrasting oceanographic conditions. Significant inter-annual variation was observed in δ13C and/or δ15N values of five of the eight prey species analysed. The strongest inter-annual variation in both δ13C and δ15N values occurred in 2015, which coincided with a strong El Niño-Southern Oscillation (ENSO). This may suggest a temporal fluctuation in the geographic source of prey or the origin of their nutrients. These results suggest that it is important to consider the potential significant differences in isotopic values within the prey assemblages that predators consume. This is important to improve the interpretation of marine predator isotope results when determining the influence of environmental variability on their diets.