Monitoring spatial and temporal chemical status of water bodies is crucial to assist environmental policy, identify the chemical fingerprints, and further reduce the source orientated pollutants. Elbe River is one of the major rivers affected by anthropogenic activities in vicinity countries. This study assessed the spatiotemporal changes in response to source shift of Cd, Cu, Ni, Pb, and Zn in the suspended particulate matter (SPM) at upstream, midstream, and downstream of the Elbe River reach in Saxony state, Germany. The average contents of trace metals in SPM was found in the order of Zn (676 mg/kg) » Pb (79 mg/kg) > Cu (74 mg/kg) > Ni (48 mg/kg) » Cd (3.2 mg/kg). According to the Mann-Kendall trend test, Cd, Cu, Pb, and Zn showed significant declines over 1998–2016. The results of source apportionment indicate industrial, urban, natural, and historical mining sources influencing the metal contents in the Elbe River of Saxony. The contributions of industrial and urban pollution decreased by 58.2% from 1998 to 2007 to 2008–2016. The contribution of the natural source was steady over the last two decades.