To develop appropriate spatial conservation planning for individual species, it is important to understand their habitat requirements and in particular to identify areas where critical life-history process such as breeding, weaning or feeding take place. The process of defining critical habitat often ignores behavioural aspects of animal distribution, which for highly migratory species like baleen whales whose feeding and breeding grounds are clearly demarcated and widely separated is not a problem. However, for other species like the endangered ‘Eastern North Pacific southern resident’ killer whale stock, critical life-history processes occur in the same waters. This killer whale stock lives in a topographically complex region (many islands) off the west coast of Canada/USA, which makes accurate mapping of densities or behaviours difficult using traditional generalised additive models. We present results on the spatial distribution of southern resident killer whale feeding grounds in 2006, using a binomial, complex region spatial smoothing model within a generalised estimating equation framework, which allows for both complex topography and correlated residuals. The model performs well and suggests a region to the south of San Juan Island as an area with a high probability of feeding, which could not have been as accurately established from a more traditional presence–absence model. We also calculate estimates of precision, which other studies did not include, enabling more informed management decisions for spatial conservation planning. A vignette containing the code along with an R workspace and function file is provided to allow the user to fit the models presented in this paper.