New Zealand sea lions Phocarctos hookeri have experienced a 46% decline in pup production in the last 25 yr, driven by female deaths in trawl fisheries around the Auckland Islands. The only colony for this species recorded away from the subantarctics and this fishing impact is on Stewart Island. Despite the Stewart Island colony only being 1% of the species, it is significant, as it is currently the only stable population and is located in an area away from most on-land human impacts, although not away from potential fisheries pressures. To ensure this colony’s persistence, more information is needed on these sea lions’ diet, foraging behaviour, and local fisheries interactions for management that promotes their protection. The present research investigates the long-term foraging behaviour, and infers the diet, of female New Zealand sea lions on Stewart Island using their known foraging behaviour and linking this to their proximal and full-length whisker stable isotope values. Previous foraging studies found that these animals have small foraging areas with consistent mesopelagic diving behaviours. These behaviours, linked with their whisker stable isotope values, show consistency in foraging behaviour and inferred diet across their entire adult life. Currently, there are no known commercial fisheries bycatch issues for sea lions around Stewart Island. However, precautionary measures ensuring fisheries pressure does not increase and management to safeguard that deepwater trawling and finfish aquaculture remain absent would be proactive steps that should be undertaken for the protection of this new colony and for this Endangered species as a whole.