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Abstract Colonial waterbirds, a major biodiversity element occurring in the core of ultra-anthropized Europe, are ideal indicators of the wellness of inland wetlands. Nonetheless, there is a critical knowledge gap in their trend and population status. We present an uninterrupted 47 years-long dataset of the breeding populations of 12 species of colonial waterbirds (Ardeidae, Phalacrocoracidae, Plataleidae, Threskiornitidae) throughout a 58,000 km2 agricultural region in the higher Po basin (NW Italy). A trained team of collaborators censused with standardized field techniques the number of nests of each species at 419 colonies in the 1972–2018 period, summing up a total of 236,316 records. Data cleaning and standardization were performed for each census year, ensuring robust and consistent data. This dataset is among the largest ever collected for a guild of European vertebrates. It has already been used to describe the factors influencing population trends, and still offers opportunities to explore a wide range of key ecological processes such as biological invasions, global change consequences and biodiversity impact of agricultural practices.