Land degradation is intense in tropical regions where it causes for instance a decline in soil fertility and reservoir siltation. Two fingerprinting approaches (i.e. the conventional approach based on radionuclide and geochemical concentrations and the alternative diffuse reflectance infrared Fourier transform spectroscopy method) were conducted independently to outline the sources delivering sediment to the river network draining into the Cointzio reservoir, in Mexican tropical highlands. This study was conducted between May and October in 2009 in subcatchments representative of the different environments supplying sediment to the river network. Overall, Cointzio catchment is characterized by very altered soils and the dominance of Andisols and Acrisols. Both fingerprinting methods provided very similar results regarding the origin of sediment in Huertitas subcatchment (dominated by Acrisols) where the bulk of sediment was supplied by gullies. In contrast, in La Cortina subcatchment dominated by Andisols, the bulk of sediment was supplied by cropland. Sediment originating from Potrerillos subcatchment characterized by a mix of Acrisols and Andisols was supplied in variable proportions by both gullies and rangeland/cropland. In this latter subcatchment, results provided by both fingerprinting methods were very variable. Our results outline the need to take the organic carbon content of soils into account and the difficulty to use geochemical properties to fingerprint sediment in very altered volcanic catchments. However, combining our fingerprinting results with sediment export data provided a way of prioritizing the implementation of erosion control measures to mitigate sediment supply to the Cointzio reservoir supplying drinking water to Morelia city. © 2012 John Wiley & Sons, Ltd.