Surface water and sediment samples from the most contaminated river in Taiwan, Houjing River, were collected for five years (2015 to 2019) and from five locations to study the contamination trends of eight heavy metals (As, Cd, Cr, Cu, Hg, Pb, Ni, and Zn). Five locations along the river were picked based on their potential of being contaminated by nearby industrial activities. The monitoring data, geo-accumulation index (${\mathit{I}}_{geo}$), contamination factor (CF), modified degree of contamination (mCd), pollution load index (PLI), and metal index (MI) were used to provide a detailed assessment of the heavy metal contamination. Demin (L3) and Chuwai (L4), two sampling sites close to the Nanzih Export Processing Zone (NEPZ) discharge points, were the most contaminated. The most contaminated periods were 2015–2016 and 2018–2019 for surface water and sediment samples, respectively. The surface water showed signs of heavy metal contamination in 2016 with mCd $>$ 1.5. For the sediment samples, the heavy metal concentration fingerprints for the five years were similar. This implied that the natural attenuation process was not adequate, and treatment technologies are required to improve sediment quality. This study provides a basis for comprehensive risk assessments and integrated environmental management measures for the river’s surface water and sediment quality. Also, it would contribute to a more inclusive evaluation of heavy metal contamination in global rivers.