Conventional fingerprinting methods based on geochemical composition still require a time-consuming and critical preliminary sample preparation. Thus, fingerprinting characteristics that can be measured in a rapid and cheap way requiring a minimal sample preparation, such as spectroscopy methods, can be a good choice for this purpose. The present study aimed to evaluate the sediment sources contribution in a rural catchment by using conventional method based on geochemical composition and an alternative method based on near-infrared diffuse reflectance (NIR) spectroscopy. This study was carried out in a rural catchment with an area of 1.19 km2 located in southern Brazil. The sediment sources evaluated were crop fields, unpaved roads and stream channels. Twenty nine suspended sediment samples were collected from nine significant storm runoff events between October 2009 and July 2011. NIR spectra of the sources and the suspended sediment samples were very similar. Nevertheless, the alternative method used to trace suspended sediment based on NIR spectroscopy was sensitive enough to detect differences in mineralogical composition of the sources materials, which were confirmed by X-ray diffraction analyses. Both conventional and alternative methods were able to discriminate the sediment sources and, despite the lack of correlation between the two methods, provided very close source ascription. The differences in the final results obtained by conventional and alternative methods are due to the nature of the variables used in each case, which are not mandatorily correlated. Efforts should be taken to try to combine both geochemical composition and near-infrared spectroscopy information on a single estimative of the sediment sources contribution in order to provide results with an even higher accuracy.