Metal contamination in aquatic environments may occur when the anthropogenic emission exceeds the natural contribution although other factors might influence the metal distribution. In the small-size Macaé river basin, most of the metal emission was originated from anthropogenic sources suggesting a contamination status. Total and exchangeable metal concentrations were determined in sediments from the pristine upstream to the urban estuary and compared to the metal content in rocks to establish contamination and background concentrations. The enrichment of Pb in sediments compared to the regional background and high exchangeable concentrations suggest the influence of anthropogenic sources on Pb distribution. Al, Fe Mn, Zn, Ba, Cu, Cr, Ni concentrations in sediments were similar to the rock content and the values were considered regional background. Spatial distribution did not follow the whole-basin emission source gradient suggesting that despite actual anthropogenic sources, the sediment mineralogy and basin geomorphology might influence the sediment metal distribution.