Mixed-species foraging aggregations of waterbirds result from foraging and anti-predator behaviors, and understanding the dynamics of these aggregations is useful in planning the conservation of waterbirds species and understanding their ecological functions within the ecosystem. This paper describes the dynamics in composition and structure of mixed-species foraging aggregations during the wet and dry seasons in the lagoon system of Las Salinas, Ciénaga de Zapata, Cuba. We surveyed these aggregations monthly from 2009 to 2017. Aggregation structure was analysed through relative abundance per guild, percentage of presence, and participation weight and participation rate. Forty-two mixed-species foraging aggregations of waterbirds were observed throughout the study, with greater species richness (n = 12 species, confidence interval: 10–13) and number of individuals (n = 800 individuals, confidence interval: 565–1,055) in the wet season. During the dry season, the most prominent species in aggregation formation were Snowy Egrets (Egretta thula), American White Ibises (Eudocimus albus) and Roseate Spoonbills (Platalea ajaja), which have been identified as nuclear species in other studies. In the wet season, American White Pelicans (Pelecanus erythrorhynchos) appeared to be the nuclear species within aggregations, something that had not previously been described in mixed-species aggregations of waterbirds. Confirming these nuclear species at Las Salinas is an important next step, given that conservation efforts focused on nuclear species might benefit the maintenance and function of the entire assembly.