The Late Holocene complex hunter-gatherers of the Lower Paraná River Basin (Argentina) settled on fluvial banks of the riparian landscape, and to a much lesser extent, on artificially elevated structures. Although both present a complex variability of burials, those of the artificial mounds are barely known. This work aims to explore the mortuary practices of the oldest artificially elevated sites in the region, Escuela 31 and Cerro Mayor (1800–1500 years BP), through a funerary taphonomic approach. We analyze the burials of 11 adult and subadult individuals of both sexes, focusing on the process of decomposition and skeletonization as consequences of mortuary treatment. The patterns of disarticulation, the presence of insect and animal damage, and cut marks are consistent with the temporal exposure of corpses and the possible use of wraps. For some cases, the spatial arrangement of the remains presented a novel type of secondary burials. The disposal of the dead comprises the ultimate stage of successive events and preparations of the corpse, which manifest complex interactions between the living and the dead. This work contributes to the knowledge about the mortuary program of South American hunter-gatherers in general and societies that built artificial mounds in the southernmost wetlands of South America. It also highlights the importance of funerary taphonomy to understand the variability of mortuary treatments.