Marine ecotourism in New Zealand presents a challenging tourism-environment management context. This is demonstrated in the case of Doubtful Sound (New Zealand) where the recent proliferation of tour operators has brought pressures to bear upon a population of bottlenose dolphins resident in the sound. Strict methodologies are necessary to objectively interpret responses to tourism-induced anthropogenic impacts upon cetaceans. Previous research in this field has established that boat interactions with dolphins in Doubtful Sound affect the behavioural budget of the dolphin population, and that dolphins are more sensitive to interactions with boats when they are resting and to a lesser extent when they are socialising. This article reports on a programme of research that employed observational data to explore the applicability of tourism management techniques grounded in spatial ecology. The data provided scientific evidence that determining critical habitat through spatio-ecological analysis is a powerful tool to protect marine mammals in New Zealand, and elsewhere, from biologically significant tourism-induced impacts. The delineation of multi-levelled marine sanctuaries may, therefore, be an effective approach to managing the impacts of tourism upon marine mammals.