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The Argentinean Mesopotamian region is a plain limited by large rivers, with an interesting environment history and climate changes, especially during late Neogene and Quaternary periods. Within the Mesopotamia, Corrientes Province is particularly attractive due toits current vegetation and geomorphological characteristics where the Eastern-Northwestern migration of the Parana River has played an important role. This migration in turn, allowed the sedimentation of the main geological units in the Pliocene-Pleistocene interval. The outcrops of the Ituzaingo (Pliocene) and Toropi/Yupoi (late Pleistocene) formations are widely distributed in Corrientes, and include numerous fossil remains of plants, invertebrates, and vertebrates (mainly mammals). Despite the paleontological and stratigraphic studies carried out, the data are still insufficient to reconstruct how the environments varied and how the migration of the Parana River could have affected the vegetation during the last part of the Cenozoic. In this contribution, the first detailed study of the phytolith assemblages is accomplished, characterizing the Ituzaingo and Toropi/Yupoi formations in order to infer the palaeoclimatic and vegetation changes during the late Cenozoic in this area of the Mesopotamian region. Four sampling localities (BV1, BV2, E1, and E2) were selected in two sites (Bella Vista and Empedrado). The recovered associations were useful for environmental reconstructions. Both formations are fluvial deposits related at different times to the current Parana River. The phytolith assemblages of the Ituzaingo Fm. evidence the different ways in which the biosilica elements were affected by pre and post-depositional processes. The Toropi/Yupoi Fm. shows well-preserved assemblages that suggest heterogeneous vegetation communities, with wetlands and grasslands to savannas and forests on the floodplain environments under seasonal subtropical climates.