Waterbirds are declining globally due to different threats that affect their abundance and shift both their breeding and wintering ranges. Cormorants disperse over vast distances during winter and are suitable indicators of the impacts of human-wildlife interactions and abiotic factors. During wintering periods, Pygmy Cormorants Microcarbo pygmaeus use regular roosts where they overnight on suitable perches, a refuge from adverse weather conditions and disturbances. Our study aimed to determine the wintering population size of the Pygmy Cormorant and its dynamics across 23-years (1996–2019) at seven roosting sites in the Maritsa River valley, Southern Bulgaria. This is a critical site for the species conservation where 3065–8180 birds are wintering annually. The wintering Pygmy Cormorant population showed a tendency to increase between 1996 and 2019 (λ = 1.03 ± 0.001). Each year Pygmy Cormorants were most abundant in December (mean ± SE, 2609 ± 185 individuals), while the lowest numbers were recorded in March (1207 ± 106). Pygmy Cormorants aggregated to roost between 4:00 PM and 5:30 PM throughout the study. The area of wintering foraging habitat of the Pygmy Cormorant increased significantly across all roosting sites in the study period from 2675.97 ha to 22564.35 ha. The number of Pygmy Cormorants at the roost was positively affected by the drop in the daily air mean temperatures and the decrease of the day length. Despite the global population increase, the Pygmy Cormorant faces a high risk of human-induced mortality during wintering and is thus regionally classified as endangered.