Ciliates are fundamental and diverse components of freshwater ecosystems. Despite their ecological importance, freshwater ciliates are understudied in Argentina, where research has primarily focused on taxonomic studies. Our investigation was conducted in Iberá (Corrientes, Argentina), one of the most significant subtropical wetlands, characterized by its vast extension and unique biodiversity. Between March 2022 and 2024, we sampled plankton from three Iberá portals: Carambola, Iberá, and San Antonio. Fixed samples were taken for quantitative analysis and live samples for qualitative analysis, along with physicochemical data. We assessed the composition of ciliates in terms of richness, analyzed β diversity to compare ciliate compositions across different portals, and estimated multiple β-diversity. A total of 69 ciliate taxa new to Iberá were identified, distributed across ten groups, with Oligohymenophorea, Spirotrichea, and Litostomatea being particularly diverse classes in the studied region. San Antonio exhibited the highest species richness (55), followed by Iberá (27) and Concepción (14). This demonstrates notable variability in species richness between different sites, suggesting habitat heterogeneity. The β diversity was high (βSOR=65%), indicating that each portal has a unique and distinct species composition from the others. This indicates a high degree of differentiation among ciliate communities in the different Iberá portals. Multiple β diversity analysis revealed that the main contributor to β diversity was species turnover (βSIM >50%). The high beta diversity and the predominance of species turnover highlight the importance of conserving multiple sites within the Iberá region to preserve the total diversity of planktonic communities, such as ciliates. Each portal contributes a unique species composition, significantly contributing to regional biodiversity, thereby emphasizing the uniqueness of planktonic ciliate communities in the Iberá region.