The dataset contains the results of a monitoring program carried out from 1972 to 2018 on the breeding populations of 12 species of colonial waterbirds (Families Ardeidae, Phalacrocoracidae, Plataleidae, Threskiornitidae) throughout an area of 58,000 square kilometers in northwestern Italy. The dataset provides estimates of the number of nests of each species, at each of the 419 breeding sites, and for each of the 47 years (a total of 236.316 data). The survey of the colonies, and the count of nests at each colony, were performed by a trained team of collaborators, using standardized field techniques and under a centralized coordination. During the five decades of monitoring, the breeding populations underwent large changes. The number of yearly active colonies increased from 45 in 1972 to 278 in 2018, and throughout the same period the five species that were breeding in 1972 were joined by seven new breeding species, including the allochthonous Sacred Ibis. The populations of herons and egrets increased greatly from 1985 to 2000, likely due to reduced human-induced mortality and to climatic variations (Fasola et al. 2010 DOI 10.1007/s10144-009-0165-1). After 2000, this positive trend reversed into a strong decline for Ardea cinerea, Egretta garzetta and Nycticorax nycticorax in the sector of the monitored area (paddies) where their main foraging habitats are rice paddies, in connection with a change in rice cultivation practices that progressively reduced the extent of flooding. Noteworthily, the same species remained stable or continued to increase in the two other sectors (rivers and uplands) where the birds forage over natural habitats.