The Cuiabá River is a major tributary of the Paraguay River; its basin is of great importance and encloses the Pantanal, the world's largest wetland. The economic base in the Cuiabá River basin is agriculture and livestock production. In order to maintain high productivity, large amounts of agricultural inputs such as pesticides are required, which may reach various environments due to several dispersion processes that occur after their introduction into the environment. Sediments play an important role in the characterization of pollution of rivers and lakes due to their potential to accumulate pollutants. The present study aimed to evaluate contamination by pesticides used on crops planted in the Rio Cuiaba basin in Mato Grosso. Accordingly, samples of bottom sediment were collected monthly from August 2011 to July 2012. We used a multi-residue method, consisting of solid-liquid extraction by mechanical agitation and purification by liquid-liquid extraction. Identification and quantification was done by gas chromatography/mass spectrometry (GC/MS) for the determination of atrazine, cypermethrin, chlorpyrifos, endosulfan (α, β and sulfate), lambda-cyhalothrin, malathion, metolachlor, metribuzin, methyl parathion, permethrin and trifuralin. Pesticide residues were identified in the samples collected in August and September 2011 and in January, February, April and July 2012, at concentrations ranging from 5.7 to 79.3 µg kg-1. Although the frequency of detection was low, these results show that there is potential for the transport of pesticides used in the Cuiabá River basin and its tributaries reaching the Pantanal.