Understanding resource utilization and economic diversification amongst Holocene hunter‐gatherers in southern Brazil requires in‐depth taphonomic analysis of faunal assemblages. Three Early to Late Holocene archaeological sites (Garivaldino, Pilger and Sangão) in Rio Grande do Sul State, southern Brazil, revealed large assemblages of small mammal (˂1 kg) remains, composed mainly of rodents. To appreciate depositional processes of fauna in relation to human consumption, taphonomic attributes and processes were evaluated. The results indicated that the remains accumulated through different antemortem taphonomic pathways, apparently linked to the size and natural history of the species represented. The small‐ and medium‐sized (<150 g) cricetid rodents (e.g. Pseudoryzomys simplex and Sooretamys angouya) were represented by a low proportion of teeth with lightly digestive corrosion suggesting that they were derived from the predatory activity of owls, possibly Tyto alba. In contrast, large‐sized cricetids (>150 g; Kunsia tomentosus, Gyldenstolpia sp. and Holochilus sp.), and several caviomorph rodents with aggregated spatial distributions (Echimyidae (†Dicolpomys fossor, Phyllomys sp., †Clyomys riograndensis and †Euryzygomatomys mordax), Caviidae (Cavia sp.) and Ctenomyidae (Ctenomys sp.)) showed evidence of thermoalteration patterns and cut marks on bones, suggesting human exploitation. A postmortem depositional environment was deduced from dendritic and branched patterns of rootlet etching, apparent mostly at Garivaldino and Pilger. Polished areas and holes on bone surfaces, and impregnation of manganese showed moderate (Sangão) or low (Garivaldino and Pilger) incidence, pointing to water transport under moderate (Pilger) and low (Garivaldino and Sangão) energy over short distances. The results obtained here provide the first clear evidence of early human exploitation of small mammals in southern Brazil, suggesting a diversification of economies. In addition, as several of the recorded rodents are today regionally or biologically extinct, a preliminary discussion about the potential impact of humans on this process is provided.