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Southeast Asia has been actively undergoing land conversion into agricultural lands over past few decades. This creates the challenges to the nation in dealing with the non-point source pollutants in many fluvial systems, thus requiring an effective approach in sediment source apportionment for an appropriate target mitigation procedure. The trace element property from different source points was used for catchment classification of Galas River. Sediment sample collection was carried out at the sources and sink areas of the catchment system. Fine sediment was analysed using X-ray fluorescence to obtain elemental composition followed by the statistical test and numerical model. Out of 83 elements, 12 elements (Mn, Ca, Cr, Ga, Dy Hf, Y, V, Th, Pb, Zn and Sr) have been selected as best tracer signatures. The solver model has indicated Pergau River as the major sediment contributor to this large catchment system. The model output could directly be proportional with the land-use practice, indicating excessive terrestrial alteration has taken place within the sites for agricultural plantation purposes. Thus, this highly recommends for the decision-making use to the targeted areas to overcome the serious sedimentation issues caused by the tillage operation in affected stream points and to improve the watershed quality.