A compound system involving three matrices (water, sediment, and paddy soil) was conceived to determine the potential sources of metal(loid)s (Ti, Fe, Co, Ni, Cu, Zn, As, Cd, Pb, and U) and synthetically evaluate their pollution levels in the Le’an River basin. The result indicated that the established background values (BVs) of paddy soil and sediment in the compound system were obviously higher than those of the upper continental crust (UCC) and soils from Jiangxi Province, a difference which was especially marked for sediment. The concentrations of Cu, Zn, As, Cd in the system had high coefficients of variation (CVs), and metal(loid)s in sediment showed higher levels than those in paddy soil, except for Pb. Cd and Cu in the system had the highest Ef levels, which probably pose a high risk to organisms and the health of local residents. There were significantly linear relationships between the site rank index (SRI) for water and that for sediment or paddy soil, revealing that matrices in the system interacted with each other. Principal component analysis (PCA) and absolute principal component scores and multiple linear regression model (APCS-MLR) results demonstrated that Cu, Zn, As, Cu, Pb, and U enrichments in the system were mainly affected by mining activities and were predominately deposited in sediment. Point pollution sources rather than non-point pollution sources such as mining activities, contributed most of the anthropogenic metal(loid)s to sediment. Both SRI and Hierarchical cluster analysis (HCA) results visually showed that S5, S8, S9, S10, S11, and S12 severe pollution grouped together and scattered through areas with extensive mining activities, while other sites with moderate pollution were spread along the main stream of the Le’an River. Display omitted •The compound system involving water, sediment and paddy soil was established.•There were latent interactions of metal(loid) among matrices in the compound system.•Cd and Cu enrichment in the compound system likely posed high risk to the organism and human health.•Sediment was the main sink of anthropogenic metal(loid)s mainly contributed by point pollution sources.•Sampling sites in the area with violent mining activities suffered severe pollution. Main finding: Establishing the compound system is an effective way to evaluate the pollution level in a specific basin. Efs indicate the migration of anthropogenic pollutants in the system.