The breeding populations of colonial herons, egrets and allied waterbirds in Northwestern Italy increased since 1972, when a long-term monitoring was initiated, up to the end of the 20° century. Populations of continental importance for some heron species were concentrated mostly in the district of intensive rice cultivation, where the paddies offered wide foraging opportunities. After 2000, new cultivation techniques caused a progressive reduction in paddy flooding. We found a significant relationship between the post-2000 decrease in the number of nests of the three most abundant species of waterbirds, Grey Heron, Little Egret and Black-crowned Night-heron, and the diminishing extent of paddy flooding estimated on satellite-derived images. On the other hand, outside the paddies district the same three species continued to increase or remained mostly stable. The recent agronomic changes in the paddies of Northwestern Italy compromise their role as surrogates of natural wetlands and their importance for environmental conservation. The spread of dry rice fields, and the consequent loss of their value for conservation of aquatic biodiversity, call for a revision of the regulations and incentives to farmers under the Common Agriculture Policy by the European Union and by local authorities. Return to early-submerged rice fields and adoption of environmental-friendly practices, such as the creation of compensatory wetlands, should become mandatory for rice to maintain its status as \“green\”\” crop.