The main approach for the conservation of wintering waterbirds is through the identification of wintering sites, the assessment of their abundance and the determination of wintering population trends. The target sites are set for the implementation of management measures for both wintering species populations and sites falling within the Natura 2000 National Ecological Network. The aim of the present study is to identify the most important waterbodies in the country, based on data from the mid-winter waterbird census during the period 1977–2021. The assessment covers 75 waterbodies falling within the following five area categories used in the MWWC—the Danube River, the North Black Sea Coast, the South Black Sea Coast, natural and artificial waterbodies in North and South Bulgaria. The assessment was made from the analysis of data on 32 species of waterfowl birds, which were split into two groups—24 common species occurring in winter (with numbers over 500 individuals recorded during the study period) and eight rare species (with total numbers less than 500 individuals). The results show that the wetlands along the Black Sea Coast, the big inland reservoirs and the Danube River are the regions most frequently inhabited by wintering waterfowl, holding the highest abundance and number of species. Conservation value indices were calculated for each site, as well as biodiversity indices like the Shannon-Winner and Simpson indices, which identified which wetlands are of greatest the importance for the protected, rare and dominant waterbird species.