In this contribution, we describe assemblages of amorphous silica microfossils from a hydromorphic paleosol of the Southern Pampas and discuss their paleoenvironmental relevance through a comparative analysis with assemblages from two modern shallow lakes. The hydromorphic paleosol analyzed, assigned to the Pliocene/Pleistocene boundary by previous studies, is exposed in the coastal cliffs of the southeastern Buenos Aires province, Argentina. The shallow lakes selected as modern analogous environments are located 4.5 kilometers away. The hydromorphic paleosol contained well-preserved silicophytoliths, whereas diatoms, chrysophycean cysts, and spicules of sponges, were found in low abundances and poorly preserved. In the modern shallow lakes, silicophytoliths were also the main component of the assemblages, being diatoms the second most abundant component. Chrysophycean cysts were found in low abundances and represented by fourteen different types of cysts, five of which are mentioned for the first time in Argentina. Spicules of sponges were rarely found, represented only by fragmented megascleres. Considering the relevance of silicophytoliths for this record, we conducted a comparative analysis that allowed us to infer temperate humid paleoclimate during the pedogenesis of the hydromorphic paleosol. This is the first study comparing the silicophytolith assemblages from a hydromorphic paleosol with a local modern analogous environment. Our results highlight the potential use of amorphous silica microfossils as bioindicators in paleosols of the Late Cenozoic pedosedimentary successions of the Southern Pampas, where the homogeneous lithology has been an obstacle for the understanding of the paleoenvironmental evolution of the region.