In Lake Superior's Pukaskwa National Park (PNP) in northern Ontario, Canada, herring gull (Larus argentatus) population size is used as an indicator of ecological integrity. Since the 1970s, gull populations have declined by 70% suggesting deteriorating park conditions. However, most other rated park indicators show stable or positive trends. Here, we focus on reconciling these seemingly disparate trends through a better understanding of factors regulating PNP gull populations. Lake-wide declines in surface-schooling prey fish may be limiting aquatic food resources for PNP gulls. To investigate this, we examined gull population trends in different parts of the park in the context of food availability. Gull diets were assessed using regurgitated pellets, egg stable isotopes (nitrogen, carbon) and fatty acids. Population declines were more severe in southern PNP compared to northern PNP and inter-region differences in bird diets likely contributed to these population trends. Gulls in the south relied to a greater extent on dwindling aquatic food resources, i.e., prey fish, while birds in northern PNP supplemented their diets with anthropogenic foods, i.e., garbage. Recognizing that regional declines in aquatic food availability have occurred across eastern Lake Superior is important for the interpretation of PNP gull population trends. Wide-scale ecological changes affecting PNP suggest that factors limiting PNP's herring gull population are not park-specific but, instead, reflect broader ecosystem-wide changes. Defining an appropriate threshold based on current knowledge of ecological conditions on Lake Superior is critical for using herring gull populations as an indicator of park ecological integrity.