Colonies of breeding waterbirds are salient biological features of many of the world’s great lakes. Globally, status of colonial waterbird populations ranges from declining and in need of conservation to maintain their roles in aquatic ecosystems, to “overabundant” and managed to reduce human-wildlife conflict; both ends of this spectrum are observed in the North American Great Lakes. Conservation and management of colonial waterbirds should rely on knowledge of colony site use dynamics because the best approach may vary depending on the frequency with which historical colony sites are abandoned and new sites colonized. The goal of this study was to understand how site use dynamics are influenced by the physical and avian social environment, using the Great Lakes Colonial Waterbird Survey as a source of breeding-season site occupancy records. This study is the first to apply community occupancy modeling techniques to colonialwaterbirds.Model parameter estimateswere generated through a Bayesian analysis using Markov chain Monte Carlo simulation. Sites with large waterbird colonies and those not susceptible to flooding were most likely to persist as breeding locations into the next survey period, and thus should be prioritized for conservation and management. Additionally, the model demonstrated that co-nester presencewas positively related to persistence probabilities, while relationships between colonization probabilities and co-nester presence ranged from positive to negative for different focal species. Finally, species-specific responses to presence of other species and to environmental influences were apparent; knowledge of this relationship variability should be incorporated into management strategies to achieve optimal outcomes.