The advance of anthropogenic activities degrades aquatic ecosystems. Testate amoebae constitute reliable bioindicators because they respond to environmental variables and reflect changes in their population dynamics. However, their study is limited in northeastern Argentina. We compared the composition and diversity of testate amoebae in anthropized and conserved lagoons in Corrientes Province, Argentina. Sampling was carried out in conserved lagoons (CL) located in Mburucuyá National Park and anthropized lagoons (AL) in the town of Mburucuyá during October 2025 and March 2026. Qualitative and quantitative fixed samples were collected, and physicochemical variables were measured in situ. Testate amoebae were identified using taxonomic literature and quantified with a Sedgwick–Rafter counting chamber under a light microscope. The Olmstead–Tukey diagram, which combines the frequency of occurrence and the mean abundance of each taxon, was applied, and a SIMPER analysis was performed to identify the taxa that contributed most to the dissimilarity between environments. AL recorded higher pH (6.5 vs. 5.8) and dissolved oxygen (4.5 vs. 3.1 mg/L), lower electrical conductivity (18.3 vs. 34 µS/cm) and total dissolved solids (9.3 vs. 17.3 ppm) than CL. AL showed greater richness (19 taxa) and abundances exceeding 3000 ind/L, whereas CL recorded 16 taxa with abundance of 2000 ind/L. Total of 12 taxa were shared between both environments, whereas 7 were exclusive to AL and 4 were exclusive to CL. Centropyxis aculeata exhibited a generalist behavior (75% frequency), whereas Arcella marginata was an occasional taxon (8%) with high abundances. C. aculeata, Netzelia corona, and A. marginata were identified as the taxa that contributed most to the dissimilarity between conserved and anthropized environments. This study highlights the potential of testate amoebae as bioindicators of environmental quality and provides new knowledge on their distribution in environments with different environmental conditions.