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European waterbird and seabird populations have been threatened by anthropogenic activities for decades. Effective strategies are needed to restore both populations and their habitats. However, the temporal period used to define the state of reference when setting restoration targets requires careful considerations to avoid the risk of shifting baseline. A risk of shifting baseline occurs if a population decreases before the time period used to set a baseline. In Europe, most bird monitoring schemes started after the 1970s, yet significant changes in population trends were already reported earlier in the 20th century. We assessed the risk of shifting baseline for 88 out of 170 waterbird and seabird species breeding in Europe. Building on historical ecology, we reconstructed population trends between 1900 and 2018 from information collected in both historical literature and monitoring scheme reports. Historical trends confirm variations in population trends for several waterbird and seabird species over the period 1900-1970, with 35 decreasing species, 38 fluctuating species, 15 increasing species and 82 species with unknown trends. A high risk of shifting baseline was identified for 28 species, for which restoration targets must consider historical trends spanning at least a century. The risk was low for 12 species, probably low for 41 species, probably high for 7 species and uncertain for 82 species. Our study highlights the crucial role of historical data collected prior to the large-scale implementation of standardized abundance monitoring, as it allows for the identification of appropriate baselines to guide the restoration of waterbird and seabird breeding populations.