Birds are among the most important biological components of wetlands. They play a key role in their ecology and are an important cultural resource for the public, in part because some species can be legally hunted. The conservation of waterbirds is especially important in terms of land use planning, in light of their ecological, cultural, and economic value. Here we summarize the results of wintering waterbirds censuses carried out in Lombardy between 2002 and 2013, using the standardized International Waterbird Census methodology. Our goals were to identify priority sites for waterbirds; estimate population sizes; define demographic trends; and provide a technical framework for making administrative and legislative decisions on the management and conservation of wetlands and their bird species. Lombardy hosts substantial numbers of wintering waterbirds, and many of its wetlands qualify as areas of conservation interest under Ramsar Convention criteria, as they host >1% of the Italian population of one or more species. Trends for the 20 species of highest conservation or hunting interest showed stable or increasing populations in most cases, with the exception of Black-necked Grebe, Common Pochard, and Eurasian Coot, which instead decreased in 2002-2013. The favourable population trends for most species suggest that the ecological status of Lombardy’s wetlands is essentially stable, but it could be improved by simple measures to improve the natural value of the shorelines and bottoms of major lakes and flooded gravel pits. Hunting was one of the main factors affecting the distribution and abundance of wintering waterbirds, which concentrate in protected areas - over 50% of all birds, rising to over 70% for species of conservation interest concentrate there, despite the fact that protected areas only account for 43% of sites surveyed. Overall, protected areas hosted bird densities that were almost seven times higher than those managed primarily for hunting, while mixed-use areas hosted intermediate densities of birds. The presence of protected and unprotected areas within the same wetland mitigates the effects of hunting on bird populations and species diversity, and may help maintain adequate conditions for their conservation.