Wetlands currently have high rates of degradation, with more than 70% lost globally. In the central Monte Desert, Argentina, they are a scarce and limited resource for the biodiversity which depends on them. Waterbirds have been used as biological indicators of wetlands because they respond to fluctuations in food resources and to environmental changes in the short term. Here we analyse the seasonal variations in the structure of the waterbird assemblage from a relict wetland in this region. We carried out censuses of waterbirds in a 6-year period (between 2009 and 2019) during the southern summer and winter. We recorded 1875 individuals of 33 species of waterbirds during the summer and 677 individuals of 29 species during the winter. The grouping patterns of the waterbird assemblages differed between seasons (R = 0.35; p < 0.01). Taxonomic diversity profiles showed greater diversity for all indexes (qD) during the summer. The guild of invertivorous and omnivorous waders had a greater abundance of individuals during the summer (p < 0.05) and, together with the surface-feeding herbivores, contributed to the 87% of the dissimilarity of the assemblages between seasons. Phoenicopterus chilensis was the only species registered as threatened with national and international extinction. Relict wetlands, such as Laguna del Viborón, still have attributes of community diversity and represent the last refuges for waterbirds of the central Monte Desert. The information gathered in this study will contribute to the guidelines for integrated management plans and monitoring programmes for the conservation of the wetland and its biodiversity.