In rivers and other freshwater bodies, the presence of mercury can be due to direct contamination by anthropic activities such as gold mining. However, it can also be attributed to atmospheric deposition and erosion, runoff, or lixiviation from surrounding soils. In the case of the Amazon rainforest, high mercury contents have been reported for litter and topsoil, which could affect the mercury concentrations in water bodies. Samples of suspended particulate matter were obtained from a transect of the Itenez River, associated lakes, and some of its tributaries. The aim was to obtain information on particulate mercury’s origin in the study area and determine the relationship between particulate mercury and particulate organic carbon. The concentration of mercury, organic matter, and the C:N ratio of the suspended matter was determined. The concentration of particulate mercury by water volume depended on changes in suspended matter loads, which in turn were mostly affected by the nature of the watershed or sediment resuspension. The observed values for the percentage of organic matter and the C:N ratio suggest that most of the mercury content in rivers and lakes originated from soils. A positive correlation was found between mercury concentration by weight of particulate matter and organic carbon content in particles. This correlation might be due to the direct binding of mercury to organic matter through functional groups like thiols or to an indirect effect of oxyhydroxides that can adsorb mercury and are associated with organic matter.