Fluctuations in size and turnover of centralized, aggregative breeding locations are attributable to both natural and anthropogenic causes, and distinguishing between these sources is critical for successful conservation and management of colonially breeding animals. We used a 40-year data set to examine the relative importance of colony variables to colony dynamics of endangered Wood Storks (Mycteria americana) within the United States. Larger colonies were less prone to abandonment and those of greater longevity were more likely to re-colonize, suggesting size and previous history have intrinsic value to Wood Storks. Colonies with a higher degree of physical connection to the mainland were more likely to be abandoned, probably because the isolation reduces access for mammalian nest predators. Proximity to human activity was positively related to the probability of re-colonization, indicating either that Wood Storks and humans are attracted to similar ecological features, or that there may be some positive benefit from nesting near human activities. Local rainfall in the 12 months prior to nest initiation was positively related to re-colonization rates and negatively related to extinction rates, suggesting that colony-site effects on persistence are mediated by annual weather patterns. Our findings present means to prioritize conservation efforts for colonial nesting waterbirds.