The phytolith assemblages of the El Palmar Formation (Late Pleistocene) are presented together with general stratigraphic and sedimentological data. The El Palmar Formation represents a channel system of the Uruguay river (South America) with longitudinal sandy gravel and gravelly sand bedforms, and associated floodplain deposits. The phytolith content of the unit was analyzed along the profiles on the right bank of the river in the middle reach (eastern Entre Ríos province, Argentina). Four outcropping profiles of the El Palmar Fm. were selected for detailed analyses: Santa Ana (Federación department), La Chola quarry, El Palmar National Park and Nueva Escocia (Colón department) localities. The herbaceous palaeoflora of the El Palmar Fm. is represented by mixed environments, such as meso-megathermic grassland with the presence of palm trees in a savanna ecosystem and micro-environments with aquatic plants and bamboo grasses that characterized a stratified forest in humid environments with high water availability. The reconstructed vegetation pattern is composed of a stratified gallery forest changing to temperate savanna, extended along the upper basin of the Uruguay river and occupying the river valley in the middle reach of the basin. The data contribute to the palaeobiodiversity knowledge of Quaternary fluvial sedimentary units of South America. In addition, the results give a better understanding of the evolutionary history of some vegetal communities, and especially the present palm trees of the El Palmar National Park reserve, as part of a relict flora that has inhabited the area since, at least, the Upper Pleistocene. The geological and micro-paleobotanical records of the El Palmar Fm. lead to the inference of general warm and humid conditions during most of the deposition of the formation, probably covering part of the last major interglacial period before the present (MIS 5).