Many studies have determined the concentration of trace elements in river sediments in Brazil. Notwithstanding, mercury assessments are scarce, especially because of exclusive extraction techniques and expensive analysis techniques. Still, this element is known for its toxicity, persistence, and bioaccumulation, making its presence in the environment an important factor for biota and human health. For this reason, the objective of this study was to determine the mercury concentration in the sediment of the Pelotas River basin, located on the border of the states of Santa Catarina and Rio Grande do Sul. The sediment was collected at eight locations of the Pelotas basin and, after drying, the mercury was quantified by atomic absorption spectrometry based on the Zeeman-background correction, coupled to a pyrolysis reactor. The mercury concentrations in the sediments of the Pelotas River varied from 40.5 ng g-1 to 62.0 ng g-1 and presented a positive correlation with the fraction of silt and clay. The concentrations of mercury found in sediments of the Pelotas River basin have a low probability of negatively affecting the biota. Nonetheless, given the persistence and bioaccumulation potential of this element, the aforementioned region needs further studies to quantify the risks it may cause on the local biota and human health.