The Niterói and Talismã sites comprise two of the most important fossiliferous deposits of the Neogene in Brazil. After 30 years of research, these sites have revealed rich assemblages of vertebrates and provided a glimpse of the Amazonian fauna and environment during the Miocene. Despite this, detailed studies that attempt to explain the genesis of these bonebeds are still scarce and hamper more robust paleoenvironmental and paleoecological reconstructions. Here we provide the first in-depth taphonomic analysis for both locations. Sedimentological and taphonomic evidence suggest that the depositional environments of Niterói and Talismã were similarly represented by shallow and calm waters in lacustrine/swampy contexts. We propose that the accumulation of bones and teeth is the result of attritional (day-to-day) mortality of organisms of the local community in a low sedimentation environment. The thanatocoenosis was exposed to biostratinomic processes for longer periods of time, which explains the high disarticulation, disassociation, fragmentation and loss of skeletal elements. The almost absence of weathering indicates that the aquatic environment slowed down the organic degradation of bioclasts, while the rarity of abrasion shows a limited influence of hydraulic flows in transporting and remobilizing bioclasts. Thus, both sites preserve mostly autochthonous to parautochthonous bioclasts, with a moderate level of time-averaging. Our results corroborate the hypothesis that lentic environments can present remarkable preservational conditions for the formation of attritional accumulations of vertebrate remains. Moreover, we show how the different collecting methods affect the description of preservational features and taphonomic interpretations of both fossil assemblages.