Metal accumulation in sediments threatens adjacent ecosystems due to the potential of metal mobilization and the subsequent uptake into food webs. Here, contents of heavy metals (Cd, Cr, Cu, Ni, Pb, and Zn) and trace elements (Ga, In, Mo, and Se) were determined for river waters and bed sediments that received sewage discharged from traditional and semiconductor industries. We used principal component analysis (PCA) to determine the metal distribution in relation to environmental factors such as pH, EC, and organic matter (OM) contents in the river basin. While water PCA categorized discharged metals into three groups that implied potential origins of contamination, sediment PCA only indicated a correlation between metal accumulation and OM contents. Such discrepancy in metal distribution between river water and bed sediment highlighted the significance of physical-chemical properties of sediment, especially OM, in metal retention. Moreover, we used Se XANES as an example to test the species transformation during metal transportation from effluent outlets to bed sediments and found a portion of Se inventory shifted from less soluble elemental Se to the high soluble and toxic selenite and selenate. The consideration of environmental factors is required to develop pollution managements and assess environmental risks for bed sediments.