Many migratory species have experienced severe population declines, but the genetic consequences of such declines are still rarely assessed. The last Central European population of gull-billed terns (Gelochelidon nilotica) has declined from 500 breeding pairs in the 1940s to 52 in 2025, whereas Mediterranean populations of this migratory waterbird still thrive. Here, we compare whole-genome sequencing (WGS) data among the declining population, two thriving populations and the ancestors of the declining population. We find comparable nucleotide diversity, but lower observed heterozygosity in the Central European population compared to the Mediterranean populations. The contemporary samples show some population structure as well, although admixture analyses and low genetic differentiation (F_ST) still suggest potential population connectivity. Museum specimens from the historic population reveal an increased level of genetic diversity compared to the contemporary population, with effective population size estimates suggesting two past population declines. While inbreeding coefficients (F_ROH) in the current Central European population are significantly higher than in the historic population, they are similar to those in the Mediterranean populations. These results suggest that population structure may be emerging, and that although inbreeding is not yet at worrisome levels in the last Central European population of gull-billed terns, it may be on the rise. If this endangered population remains small and isolation manifests, the effects of inbreeding depression may become more pronounced over time, potentially reducing fitness and increasing the risk of extinction.