ABSTRACT In the Tsitsa River catchment of the Eastern Cape Province, South Africa, concerns regarding the sedimentation of a proposed large, multipurpose, in-channel water storage scheme prompted investigations of sub-catchment suspended sediment loads and yields. Confluence-based fingerprinting and source apportionment was undertaken to explore whether this simple approach could identify relative sub-catchment contributions to downstream sediment loads, supplementing modelling and direct sampling. In November 2018, fine sediment sequestered in bed substrates was sampled above and below confluences, using a resuspension technique. The < 63 µm sample fraction underwent analysis of mineral magnetic properties, gamma emitting radionuclide activities and geochemistry to identify suitable tracers. Conservatism and range tests were used to select different combinations of composite fingerprints at seven confluences. Bivariate source apportionment using an unmixing model showed that the approach could be used as a preliminary means of determining relative sub-catchment sediment contributions. Catchment characteristics such as geology and land cover, as well as land tenure and management, were considered as explanatory factors for the difference in sediment contributions. The results for most sub-catchments were broadly similar to those from other studies. Shortcomings of this approach included the reliance on a single sampling effort, and uncertainty associated with sub-catchment sediment transport and residence times.