Human activities in marine coastal areas may coincide with protected areas for birds. Some of these anthropogenic activities may pose threats, such as gillnet fisheries, which can significantly affect populations of diving birds, especially gregarious species that gather in huge flocks in small areas such as Greater Scaup (Aythya marila). The Odra Estuary (Baltic Sea, Poland) is known for its importance as a wintering site for scaup; it is also used by fishermen using gillnets. Precise tools to determine the distribution and abundance of birds allow evaluation of risks faced by large aggregations. We used kernel density interpolation to estimate the spatial density of scaup in the Odra Estuary in spring 2011. At that time, an extraordinarily high number of scaup (95,400) was recorded, ∼73% (63.0–94.5%) of the entire northwest European flyway population. Three variables are particularly important for conserving highly mobile long-distance migrating species: spatial distribution, abundance, and time (season of the year). This event concentrated most of the scaup flyway population in a small space, making the population vulnerable to mass mortality. We also show aggregated data of the spatial distribution of scaup during the 2015–2016 and 2016–2017 seasons to highlight differences in the spatial use of the area between seasons. Vast areas occupied by scaup in 2011 were not used during 2 other studied seasons; this spatial variation may be crucial in conservation planning of this species. Our results are a first step in documenting the spatial distribution of scaup in the Odra Estuary and identifying the potential area of overlap with fishing activity.