Invasive mammal eradications are widely used for managing island ecosystems. However, tracking the outcomes of such large-scale, whole ecosystem projects is challenging and costly, and monitoring all components of an ecosystem is near impossible. Instead, indicators of ecosystem change may provide more practical and integrated measures of ecosystem response to eradications. As high-order marine predators, seabirds subsidise island ecosystems with nutrients isotopically enriched in nitrogen. Invasive mammals have caused a global decline of seabirds on islands, reducing this nutrient subsidisation. Following eradications, nitrogen stable isotope analysis may provide a useful and resource-efficient indicator of ecosystem functional change on eradicated islands. However, isotope ratios are affected by a myriad of factors, with potential sources of variation being introduced by spatial and temporal variation in sampling, and within and between different taxa and ecosystem components. To correctly attribute isotopic change to post-eradication ecosystem function change, these confounding variables need to be understood. To address this need, we analysed stable isotopes of nitrogen in soil, plant, spider, and seabird guano samples collected at different distances from seabird colonies and at different stages of the short-tailed shearwater breeding cycle on six island sites around south-eastern Tasmania, Australia. Across these cool, temperate islands we detected no temporal variability in δ15N throughout the breeding season. However, there was notable spatial variability in δ15N values. The effects of seabird-derived nutrient subsidisation were highly localised with high δ15N values found inside seabird colonies and then rapidly decreasing from the colony boundary. Higher δ15N values also occurred in areas of higher burrow density within a colony. Variability in δ15N values also existed both within and between ecosystem components. Our results highlight the importance of context dependency when using ecological indicators and have important implications for the design, implementation and interpretation of studies employing stable isotopes as indicators for ecosystem change. We provide recommendations for designing future stable isotope studies on seabird islands.