In the Kerguelen Islands, the multiple effects of climate change are expected to impact coastal marine habitats. Species distribution models (SDM) can represent a convenient tool to predict the biogeographic response of species to climate change but biotic interactions are not considered in these models. Nevertheless, new species interactions can emerge in communities exposed to environmental changes and the structure of biotic interactions is directly related to the potential resilience of ecosystems. Trophic interaction studies can help predict species vulnerability to environmental changes using carbon (δ13C) and nitrogen (δ15N) stable isotope ratios to generate trophic models. Using new available data inputs, we generated robust SDM and trophic interaction models to assess the potential response and sensitivity of three echinoid species to future worst-case scenarios of environmental change in the Kerguelen Plateau region. The two modelling approaches provide contrasting insights into the potential responses of each species to future environmental changes with both approaches identifying Abatus cordatus to be particularly vulnerable due to its narrow ecological niche and endemism to near-shore areas. Coupling insights gained from trophic niche ecology with species distribution modelling represents a promising approach that can improve our understanding and ability to predict the potential responses of species to future habitat changes.